diff --git a/README.md b/README.md
index 4a757dc04f1fa3ed3d69f4298018fd6e63562d43..3f7e9c2cfa91e07f43c20a39b755603734ba9c3d 100644
--- a/README.md
+++ b/README.md
@@ -44,7 +44,7 @@ You will need to install the required programs listed in the following table, or
| _fqconvert_ <br> _fqduplicate_ <br> _fqextract_ <br> _fqstats_ | [fqtools](http://ftp.pasteur.fr/pub/gensoft/projects/fqtools/) | ≥ 1.1a | [ftp.pasteur.fr/pub/gensoft/projects/fqtools](http://ftp.pasteur.fr/pub/gensoft/projects/fqtools/) |
| [_Musket_](http://musket.sourceforge.net/homepage.htm)<sup> ✦</sup> | - | ≥ 1.1 | [sourceforge.net/projects/musket](https://sourceforge.net/projects/musket/) |
| [_ntCard_](https://www.bcgsc.ca/resources/software/ntcard) | - | > 1.2 | [github.com/bcgsc/ntCard](https://github.com/bcgsc/ntCard) |
-| [_ROCK_](https://research.pasteur.fr/en/software/rock) | - | ≥ 1.9.3 | [gitlab.pasteur.fr/vlegrand/ROCK](https://gitlab.pasteur.fr/vlegrand/ROCK) |
+| [_ROCK_](https://research.pasteur.fr/en/software/rock) | - | ≥ 2.1 | [gitlab.pasteur.fr/vlegrand/ROCK](https://gitlab.pasteur.fr/vlegrand/ROCK) |
</div>
@@ -125,7 +125,7 @@ Run _fqCleanER_ without option to read the following documentation:
-b <string> base name for output files (mandatory option)
-a <infile> to set a file containing every alien oligonucleotide sequence (one per line) to
be clipped during step 'T' (see below)
- -a <string> one or several key words (separated with commas), each corresponding to a set
+ -a <string> one or several key words (separated with commas), each corresponding to a set
of alien oligonucleotide sequences to be clipped during step 'T' (see below):
POLY nucleotide homopolymers
NEXTERA Illumina Nextera index Kits
@@ -138,22 +138,22 @@ Run _fqCleanER_ without option to read the following documentation:
TRUSEQ_SMALLRNA Illumina TruSeq Small RNA Kits
Note that these sets of alien sequences are not exhaustive and will never
replace the exact oligos used for library preparation (default: "POLY")
- -a AUTO to perform de novo inference of 3' alien oligonucleotide sequence(s) of at
- least 20 nucleotide length; selected sequences are completed with those from
- "POLY" (see above)
- -A <infile> to set sequence or k-mer model file(s) to carry out contaminant read removal
- during step 'C'; several comma-separated file names can be specified; allowed
+ -a AUTO to perform de novo inference of 3' alien oligonucleotide sequence(s) of at
+ least 20 nucleotide length; selected sequences are completed with those from
+ "POLY" (see above)
+ -A <infile> to set sequence or k-mer model file(s) to carry out contaminant read removal
+ during step 'C'; several comma-separated file names can be specified; allowed
file extensions: .fa, .fasta, .fna, .kmr or .kmz (default: phiX174 genome)
-d <string> displays the alien oligonucleotide sequences corresponding to the specified key
word(s); see option -a for the list of available key words
- -q <int> quality score threshold; all bases with Phred score below this threshold are
+ -q <int> quality score threshold; all bases with Phred score below this threshold are
considered as non-confident (default: 15)
-l <int> minimum required length for a read (default: half the average read length)
- -p <int> maximum allowed percentage of non-confident bases (as ruled by option -q) per
+ -p <int> maximum allowed percentage of non-confident bases (as ruled by option -q) per
read (default: 50)
-c <int> minimum allowed coverage depth for step 'L' or 'N' (default: 4)
-C <int> maximum allowed coverage depth for step 'R' or 'N' (default: 90)
- -s <string> a sequence of tasks to be iteratively performed, each being defined by one of
+ -s <string> a sequence of tasks to be iteratively performed, each being defined by one of
the following uppercase characters:
C discarding [C]ontaminating reads (as ruled by option -A)
E correcting sequencing [E]rrors
@@ -199,7 +199,7 @@ Run _fqCleanER_ without option to read the following documentation:
<span style="color:navy; font-size:1.1em;">**[T]**</span> Trimming and clipping (`-s T`) are performed using [_AlienTrimmer_](https://research.pasteur.fr/en/software/alientrimmer/) (Criscuolo and Brisse 2013). Clipping is carried out based on the specified alien oligonucleotides (option `-a`), where alien oligonucleotide sequences can be (i) set using precomputed standard library names, (ii) specified via user-defined FASTA-formatted file, or (iii) directly estimated from the input files using [_AlienDiscover_](https://gitlab.pasteur.fr/GIPhy/AlienDiscover) (option `-a AUTO`). When step T is run without setting option `-a`, clipping is carried out with the four homopolymers (`POLY`) as alien oligonucleotides. Trimming is carried out by deleting 5' and 3' regions containing many non-confident bases, where a base is considered as non-confident when its Phred score is lower than a Phred score threshold (set using option `-q`; default: 15). After trimming/clipping an HTS read, it can be discarded when the number of remaining bases is lower than a specified length threshold (option `-l`; default: half the average read length) or when the percentage of remaining non-confident bases is higher than another specified threshold (option `-p`; default: 50%). Note that when HTS read discarding breaks PE, singletons are written into dedicated output files ( _.S.fastq_ file extension).
-* Each predefined set of alien oligonucleotide sequences can be displayed using option `-d`. Some sets of alien oligonucleotide sequences are derived from _'Illumina Adapter Sequences'_ [Document # 1000000002694 v16](https://emea.support.illumina.com/downloads/illumina-adapter-sequences-document-1000000002694.html), i.e. options `-a NEXTERA` (_Nextera DNA Indexes_), `-a IUDI` (_IDT for Illumina UD Indexes_), `-a AMPLISEQ` (_AmpliSeq for Illumina Panels_), `-a TRUSIGHT_PANCANCER` (_TruSight RNA Pan-Cancer Panel_), `-a TRUSEQ_UD` (_IDT for Illumina-TruSeq DNA and RNA UD Indexes_), `-a TRUSEQ_CD` (_TruSeq DNA and RNA CD Indexes_), `-a TRUSEQ_SINGLE` (_TruSeq Single Indexes_), and `-a TRUSEQ_SMALLRNA` (_TruSeq Small RNA_). <br> <sup><sub>**[Oligonucleotide sequences © 2021 Illumina, Inc. All rights reserved. Derivative works created by Illumina customers are authorized for use with Illumina instruments and products only. All other uses are strictly prohibited.]**</sub></sup>
+* Each predefined set of alien oligonucleotide sequences can be displayed using option `-d`. Some sets of alien oligonucleotide sequences are derived from _'Illumina Adapter Sequences'_ [Document # 1000000002694 v20](https://support-docs.illumina.com/SHARE/AdapterSequences/Content/SHARE/FrontPages/AdapterSeq.htm), i.e. options `-a NEXTERA` (_Nextera DNA Indexes_), `-a IUDI` (_IDT for Illumina UD Indexes_), `-a AMPLISEQ` (_AmpliSeq for Illumina Panels_), `-a TRUSIGHT_PANCANCER` (_TruSight RNA Pan-Cancer Panel_), `-a TRUSEQ_UD` (_IDT for Illumina-TruSeq DNA and RNA UD Indexes_), `-a TRUSEQ_CD` (_TruSeq DNA and RNA CD Indexes_), `-a TRUSEQ_SINGLE` (_TruSeq Single Indexes_), and `-a TRUSEQ_SMALLRNA` (_TruSeq Small RNA_). <br> <sup><sub>**[Oligonucleotide sequences © 2021-2025 Illumina, Inc. All rights reserved. Derivative works created by Illumina customers are authorized for use with Illumina instruments and products only. All other uses are strictly prohibited.]**</sub></sup>
## References
diff --git a/fqCleanER.sh b/fqCleanER.sh
index d0b1b363769932ebe03fd0ca25945f18dd9fa95e..f452625e4faaa04503bbd3261b0d87100ef48c9b 100755
--- a/fqCleanER.sh
+++ b/fqCleanER.sh
@@ -4,7 +4,7 @@
# #
# fqCleanER: fastq file Cleaning and Enhancement Routine #
# #
- COPYRIGHT="Copyright (C) 2015-2023 Institut Pasteur" #
+ COPYRIGHT="Copyright (C) 2015-2025 Institut Pasteur" #
# #
# This program is free software: you can redistribute it and/or modify it under the terms of the GNU #
# General Public License as published by the Free Software Foundation, either version 3 of the License, or #
@@ -20,9 +20,25 @@
# Contact: #
# Alexis Criscuolo alexis.criscuolo@pasteur.fr #
# Genome Informatics & Phylogenetics (GIPhy) giphy.pasteur.fr #
-# Centre de Ressources Biologiques de l'Institut Pasteur (CRBIP) research.pasteur.fr/en/b/VTq #
+# Centre de Ressources Biologiques de l'Institut Pasteur (CRBIP) crbip.pasteur.fr #
# Institut Pasteur, Paris, FRANCE research.pasteur.fr #
# #
+# 4888888883 #
+# 48800007 4003 1 #
+# 4880000007 400001 83 101 100 01 4000009 888888888 101 888888888 08 80 888888888 #
+# 4000000008 8000001 83 181 10101 01 601 1 181 181 181 08 80 181 #
+# 40000000008 8000001 803 181 10 101 01 60003 181 181 181 08 80 181 #
+# 100888880008 800007 60003 181 10 10101 4 109 181 181 181 68 87 181 #
+# 81 68888 80887 600008 101 10 001 0000007 101 101 101 600009 101 #
+# 808883 1 887 6000008 #
+# 8000000003 480000008 #
+# 600000000083 888000000007 10000000 40 4000009 888888888 10000000 08 80 1000000 #
+# 60000000008 80000000007 180 39 4000 601 1 181 10 08 80 10 39 #
+# 6000000008 8000000007 18000007 47 00 60003 181 1000000 08 80 1000007 #
+# 680000008 800000087 180 40000000 4 109 181 10 68 87 10 06 #
+# 6888008 8000887 100 47 00 0000007 101 10000000 600009 10 00 #
+# 688 8887 #
+# #
##############################################################################################################
##############################################################################################################
@@ -31,7 +47,16 @@
# = VERSIONS = #
# ============ #
# #
- VERSION=23.12 #
+ VERSION=25.03 #
+# + fixed mini bug in fqmerge with PE lib3 #
+# + updated TMPDIR management #
+# + updated trap #
+# + updated list of alien oligos (Illumina Unique Dual Indexes V3) #
+# #
+# VERSION=25.01 #
+# + fixed mini bug when displaying lib3 initial content #
+# #
+# VERSION=23.12 #
# + fixed bug in fqinit() when dealing with Phred lines containing only '?' (e.g. SRR26898806) #
# #
# VERSION=23.07 #
@@ -344,6 +369,7 @@ EOF
# #
# -- IUDI: Illumina Unique Dual Indexes ------------------------------------------------------------------- #
# derived from: Illumina Adapter Sequences (Document # 1000000002694 v16; pp. 2-27) #
+# Illumina Adapter Sequences (Document # 1000000002694 v20) #
# > Oligonucleotide sequences © 2021 Illumina, Inc. All rights reserved. Derivative works #
# created by Illumina customers are authorized for use with Illumina instruments and #
# products only. All other uses are strictly prohibited. #
@@ -373,6 +399,10 @@ AATGATACGGCGACCACCGAGATCTACACctacaagataTCGTCGGCAGCGTC
CAAGCAGAAGACGGCATACGAGATatatgagacgGTCTCGTGGGCTCGG
>Illumina UD IDT Index 2 (i5) Adapter UDP0003
AATGATACGGCGACCACCGAGATCTACACtatagtagctTCGTCGGCAGCGTC
+>Illumina UD IDT Index 1 (i7) Adapter UDP0003V3
+CAAGCAGAAGACGGCATACGAGATtcggatgtcgGTCTCGTGGGCTCGG
+>Illumina UD IDT Index 2 (i5) Adapter UDP0003V3
+AATGATACGGCGACCACCGAGATCTACACtacgttcattTCGTCGGCAGCGTC
>Illumina UD IDT Index 1 (i7) Adapter UDP0004
CAAGCAGAAGACGGCATACGAGATcttatggaatGTCTCGTGGGCTCGG
>Illumina UD IDT Index 2 (i5) Adapter UDP0004
@@ -381,6 +411,10 @@ AATGATACGGCGACCACCGAGATCTACACtgcctggtggTCGTCGGCAGCGTC
CAAGCAGAAGACGGCATACGAGATtaatctcgtcGTCTCGTGGGCTCGG
>Illumina UD IDT Index 2 (i5) Adapter UDP0005
AATGATACGGCGACCACCGAGATCTACACacattatcctTCGTCGGCAGCGTC
+>Illumina UD IDT Index 1 (i7) Adapter UDP0005V3
+CAAGCAGAAGACGGCATACGAGATtcctattgtgGTCTCGTGGGCTCGG
+>Illumina UD IDT Index 2 (i5) Adapter UDP0005V3
+AATGATACGGCGACCACCGAGATCTACACtccatccgagTCGTCGGCAGCGTC
>Illumina UD IDT Index 1 (i7) Adapter UDP0006
CAAGCAGAAGACGGCATACGAGATgcgcgatgttGTCTCGTGGGCTCGG
>Illumina UD IDT Index 2 (i5) Adapter UDP0006
@@ -545,6 +579,10 @@ AATGATACGGCGACCACCGAGATCTACACccataaggttTCGTCGGCAGCGTC
CAAGCAGAAGACGGCATACGAGATtaatggatctGTCTCGTGGGCTCGG
>Illumina UD IDT Index 2 (i5) Adapter UDP0046
AATGATACGGCGACCACCGAGATCTACACatctctaccaTCGTCGGCAGCGTC
+>Illumina UD IDT Index 1 (i7) Adapter UDP0046V3
+CAAGCAGAAGACGGCATACGAGATtccatgttgcGTCTCGTGGGCTCGG
+>Illumina UD IDT Index 2 (i5) Adapter UDP0046V3
+AATGATACGGCGACCACCGAGATCTACACcttgtcttaaTCGTCGGCAGCGTC
>Illumina UD IDT Index 1 (i7) Adapter UDP0047
CAAGCAGAAGACGGCATACGAGATtatccaggacGTCTCGTGGGCTCGG
>Illumina UD IDT Index 2 (i5) Adapter UDP0047
@@ -573,18 +611,34 @@ AATGATACGGCGACCACCGAGATCTACACgtgcgtccttTCGTCGGCAGCGTC
CAAGCAGAAGACGGCATACGAGATttacaattccGTCTCGTGGGCTCGG
>Illumina UD IDT Index 2 (i5) Adapter UDP0053
AATGATACGGCGACCACCGAGATCTACACagcacatcctTCGTCGGCAGCGTC
+>Illumina UD IDT Index 1 (i7) Adapter UDP0053V3
+CAAGCAGAAGACGGCATACGAGATtaccgaactaGTCTCGTGGGCTCGG
+>Illumina UD IDT Index 2 (i5) Adapter UDP0053V3
+AATGATACGGCGACCACCGAGATCTACACccatgtgtagTCGTCGGCAGCGTC
>Illumina UD IDT Index 1 (i7) Adapter UDP0054
CAAGCAGAAGACGGCATACGAGATaagcttatgcGTCTCGTGGGCTCGG
>Illumina UD IDT Index 2 (i5) Adapter UDP0054
AATGATACGGCGACCACCGAGATCTACACttccgtcgcaTCGTCGGCAGCGTC
+>Illumina UD IDT Index 1 (i7) Adapter UDP0054V3
+CAAGCAGAAGACGGCATACGAGATgtagtaatagGTCTCGTGGGCTCGG
+>Illumina UD IDT Index 2 (i5) Adapter UDP0054V3
+AATGATACGGCGACCACCGAGATCTACACgagtctctccTCGTCGGCAGCGTC
>Illumina UD IDT Index 1 (i7) Adapter UDP0055
CAAGCAGAAGACGGCATACGAGATtattcctcagGTCTCGTGGGCTCGG
>Illumina UD IDT Index 2 (i5) Adapter UDP0055
AATGATACGGCGACCACCGAGATCTACACcttaaccactTCGTCGGCAGCGTC
+>Illumina UD IDT Index 1 (i7) Adapter UDP0055V3
+CAAGCAGAAGACGGCATACGAGATggttatgctaGTCTCGTGGGCTCGG
+>Illumina UD IDT Index 2 (i5) Adapter UDP0055V3
+AATGATACGGCGACCACCGAGATCTACACgctatgcgcaTCGTCGGCAGCGTC
>Illumina UD IDT Index 1 (i7) Adapter UDP0056
CAAGCAGAAGACGGCATACGAGATctcgtgcgttGTCTCGTGGGCTCGG
>Illumina UD IDT Index 2 (i5) Adapter UDP0056
AATGATACGGCGACCACCGAGATCTACACgcctcggataTCGTCGGCAGCGTC
+>Illumina UD IDT Index 1 (i7) Adapter UDP0056V3
+CAAGCAGAAGACGGCATACGAGATacaatagagtGTCTCGTGGGCTCGG
+>Illumina UD IDT Index 2 (i5) Adapter UDP0056V3
+AATGATACGGCGACCACCGAGATCTACACatcgcatatgTCGTCGGCAGCGTC
>Illumina UD IDT Index 1 (i7) Adapter UDP0057
CAAGCAGAAGACGGCATACGAGATttaggatagaGTCTCGTGGGCTCGG
>Illumina UD IDT Index 2 (i5) Adapter UDP0057
@@ -637,34 +691,66 @@ AATGATACGGCGACCACCGAGATCTACACaacctagcacTCGTCGGCAGCGTC
CAAGCAGAAGACGGCATACGAGATaagtactccaGTCTCGTGGGCTCGG
>Illumina UD IDT Index 2 (i5) Adapter UDP0069
AATGATACGGCGACCACCGAGATCTACACtctgtgtggaTCGTCGGCAGCGTC
+>Illumina UD IDT Index 1 (i7) Adapter UDP0069V3
+CAAGCAGAAGACGGCATACGAGATaaggccttggGTCTCGTGGGCTCGG
+>Illumina UD IDT Index 2 (i5) Adapter UDP0069V3
+AATGATACGGCGACCACCGAGATCTACACtcgaagtactTCGTCGGCAGCGTC
>Illumina UD IDT Index 1 (i7) Adapter UDP0070
CAAGCAGAAGACGGCATACGAGATacgtcaatacGTCTCGTGGGCTCGG
>Illumina UD IDT Index 2 (i5) Adapter UDP0070
AATGATACGGCGACCACCGAGATCTACACggaattccaaTCGTCGGCAGCGTC
+>Illumina UD IDT Index 1 (i7) Adapter UDP0070V3
+CAAGCAGAAGACGGCATACGAGATtgtggagtaaGTCTCGTGGGCTCGG
+>Illumina UD IDT Index 2 (i5) Adapter UDP0070V3
+AATGATACGGCGACCACCGAGATCTACACgacaccgatgTCGTCGGCAGCGTC
>Illumina UD IDT Index 1 (i7) Adapter UDP0071
CAAGCAGAAGACGGCATACGAGATggtgtacaagGTCTCGTGGGCTCGG
>Illumina UD IDT Index 2 (i5) Adapter UDP0071
AATGATACGGCGACCACCGAGATCTACACaagcgcgcttTCGTCGGCAGCGTC
+>Illumina UD IDT Index 1 (i7) Adapter UDP0071V3
+CAAGCAGAAGACGGCATACGAGATcacttctactGTCTCGTGGGCTCGG
+>Illumina UD IDT Index 2 (i5) Adapter UDP0071V3
+AATGATACGGCGACCACCGAGATCTACACctagcgtcgaTCGTCGGCAGCGTC
>Illumina UD IDT Index 1 (i7) Adapter UDP0072
CAAGCAGAAGACGGCATACGAGATccacctgtgtGTCTCGTGGGCTCGG
>Illumina UD IDT Index 2 (i5) Adapter UDP0072
AATGATACGGCGACCACCGAGATCTACACtgagcgttgtTCGTCGGCAGCGTC
+>Illumina UD IDT Index 1 (i7) Adapter UDP0072V3
+CAAGCAGAAGACGGCATACGAGATtggactcgtaGTCTCGTGGGCTCGG
+>Illumina UD IDT Index 2 (i5) Adapter UDP0072V3
+AATGATACGGCGACCACCGAGATCTACACtagcgaagcaTCGTCGGCAGCGTC
>Illumina UD IDT Index 1 (i7) Adapter UDP0073
CAAGCAGAAGACGGCATACGAGATgttccgcaggGTCTCGTGGGCTCGG
>Illumina UD IDT Index 2 (i5) Adapter UDP0073
AATGATACGGCGACCACCGAGATCTACACatcataggctTCGTCGGCAGCGTC
+>Illumina UD IDT Index 1 (i7) Adapter UDP0073V3
+CAAGCAGAAGACGGCATACGAGATtatcatgagaGTCTCGTGGGCTCGG
+>Illumina UD IDT Index 2 (i5) Adapter UDP0073V3
+AATGATACGGCGACCACCGAGATCTACACaacacgtggaTCGTCGGCAGCGTC
>Illumina UD IDT Index 1 (i7) Adapter UDP0074
CAAGCAGAAGACGGCATACGAGATaccttatgaaGTCTCGTGGGCTCGG
>Illumina UD IDT Index 2 (i5) Adapter UDP0074
AATGATACGGCGACCACCGAGATCTACACtgttagaaggTCGTCGGCAGCGTC
+>Illumina UD IDT Index 1 (i7) Adapter UDP0074V3
+CAAGCAGAAGACGGCATACGAGATcttggcctcgGTCTCGTGGGCTCGG
+>Illumina UD IDT Index 2 (i5) Adapter UDP0074V3
+AATGATACGGCGACCACCGAGATCTACACgtgttaccggTCGTCGGCAGCGTC
>Illumina UD IDT Index 1 (i7) Adapter UDP0075
CAAGCAGAAGACGGCATACGAGATcgctgcagagGTCTCGTGGGCTCGG
>Illumina UD IDT Index 2 (i5) Adapter UDP0075
AATGATACGGCGACCACCGAGATCTACACgatggatgtaTCGTCGGCAGCGTC
+>Illumina UD IDT Index 1 (i7) Adapter UDP0075V3
+CAAGCAGAAGACGGCATACGAGATgtctcgtgaaGTCTCGTGGGCTCGG
+>Illumina UD IDT Index 2 (i5) Adapter UDP0075V3
+AATGATACGGCGACCACCGAGATCTACACagattgttacTCGTCGGCAGCGTC
>Illumina UD IDT Index 1 (i7) Adapter UDP0076
CAAGCAGAAGACGGCATACGAGATgtagagtcagGTCTCGTGGGCTCGG
>Illumina UD IDT Index 2 (i5) Adapter UDP0076
AATGATACGGCGACCACCGAGATCTACACacggccgtcaTCGTCGGCAGCGTC
+>Illumina UD IDT Index 1 (i7) Adapter UDP0076V3
+CAAGCAGAAGACGGCATACGAGATccatccacgcGTCTCGTGGGCTCGG
+>Illumina UD IDT Index 2 (i5) Adapter UDP0076V3
+AATGATACGGCGACCACCGAGATCTACACttgaccaatgTCGTCGGCAGCGTC
>Illumina UD IDT Index 1 (i7) Adapter UDP0077
CAAGCAGAAGACGGCATACGAGATggataccagaGTCTCGTGGGCTCGG
>Illumina UD IDT Index 2 (i5) Adapter UDP0077
@@ -697,6 +783,10 @@ AATGATACGGCGACCACCGAGATCTACACagacacattaTCGTCGGCAGCGTC
CAAGCAGAAGACGGCATACGAGATgtccacttgtGTCTCGTGGGCTCGG
>Illumina UD IDT Index 2 (i5) Adapter UDP0084
AATGATACGGCGACCACCGAGATCTACACgcgcgatgttTCGTCGGCAGCGTC
+>Illumina UD IDT Index 1 (i7) Adapter UDP0084V3
+CAAGCAGAAGACGGCATACGAGATtagatccagtGTCTCGTGGGCTCGG
+>Illumina UD IDT Index 2 (i5) Adapter UDP0084V3
+AATGATACGGCGACCACCGAGATCTACACtcgccgctagTCGTCGGCAGCGTC
>Illumina UD IDT Index 1 (i7) Adapter UDP0085
CAAGCAGAAGACGGCATACGAGATttaggtaccaGTCTCGTGGGCTCGG
>Illumina UD IDT Index 2 (i5) Adapter UDP0085
@@ -769,6 +859,10 @@ AATGATACGGCGACCACCGAGATCTACACtggtgcctggTCGTCGGCAGCGTC
CAAGCAGAAGACGGCATACGAGATcaggcgccatGTCTCGTGGGCTCGG
>Illumina UD IDT Index 2 (i5) Adapter UDP0102
AATGATACGGCGACCACCGAGATCTACACtccacggcctTCGTCGGCAGCGTC
+>Illumina UD IDT Index 1 (i7) Adapter UDP0102V3
+CAAGCAGAAGACGGCATACGAGATttgaagctagGTCTCGTGGGCTCGG
+>Illumina UD IDT Index 2 (i5) Adapter UDP0102V3
+AATGATACGGCGACCACCGAGATCTACACtgtgtaagctTCGTCGGCAGCGTC
>Illumina UD IDT Index 1 (i7) Adapter UDP0103
CAAGCAGAAGACGGCATACGAGATacataacggaGTCTCGTGGGCTCGG
>Illumina UD IDT Index 2 (i5) Adapter UDP0103
@@ -941,18 +1035,34 @@ AATGATACGGCGACCACCGAGATCTACACcatgtagaggTCGTCGGCAGCGTC
CAAGCAGAAGACGGCATACGAGATggccatcataGTCTCGTGGGCTCGG
>Illumina UD IDT Index 2 (i5) Adapter UDP0145
AATGATACGGCGACCACCGAGATCTACACgattgtcataTCGTCGGCAGCGTC
+>Illumina UD IDT Index 1 (i7) Adapter UDP0145V3
+CAAGCAGAAGACGGCATACGAGAaacctagcacGTCTCGTGGGCTCGG
+>Illumina UD IDT Index 2 (i5) Adapter UDP0145V3
+AATGATACGGCGACCACCGAGATCTACACtgaatattgcTCGTCGGCAGCGTC
>Illumina UD IDT Index 1 (i7) Adapter UDP0146
CAAGCAGAAGACGGCATACGAGATaattgctgcgGTCTCGTGGGCTCGG
>Illumina UD IDT Index 2 (i5) Adapter UDP0146
AATGATACGGCGACCACCGAGATCTACACattccgctatTCGTCGGCAGCGTC
+>Illumina UD IDT Index 1 (i7) Adapter UDP0146V3
+CAAGCAGAAGACGGCATACGAGATtggtcgctgtGTCTCGTGGGCTCGG
+>Illumina UD IDT Index 2 (i5) Adapter UDP0146V3
+AATGATACGGCGACCACCGAGATCTACACcaggagctctTCGTCGGCAGCGTC
>Illumina UD IDT Index 1 (i7) Adapter UDP0147
CAAGCAGAAGACGGCATACGAGATtaaggaacgtGTCTCGTGGGCTCGG
>Illumina UD IDT Index 2 (i5) Adapter UDP0147
AATGATACGGCGACCACCGAGATCTACACgaccgctgtgTCGTCGGCAGCGTC
+>Illumina UD IDT Index 1 (i7) Adapter UDP0147V3
+CAAGCAGAAGACGGCATACGAGATtctgtgtggaGTCTCGTGGGCTCGG
+>Illumina UD IDT Index 2 (i5) Adapter UDP0147V3
+AATGATACGGCGACCACCGAGATCTACACttgtcggatgTCGTCGGCAGCGTC
>Illumina UD IDT Index 1 (i7) Adapter UDP0148
CAAGCAGAAGACGGCATACGAGATctatacgcggGTCTCGTGGGCTCGG
>Illumina UD IDT Index 2 (i5) Adapter UDP0148
AATGATACGGCGACCACCGAGATCTACACtaggaaccggTCGTCGGCAGCGTC
+>Illumina UD IDT Index 1 (i7) Adapter UDP0148V3
+CAAGCAGAAGACGGCATACGAGATcctaacacttGTCTCGTGGGCTCGG
+>Illumina UD IDT Index 2 (i5) Adapter UDP0148V3
+AATGATACGGCGACCACCGAGATCTACACgctagttccgTCGTCGGCAGCGTC
>Illumina UD IDT Index 1 (i7) Adapter UDP0149
CAAGCAGAAGACGGCATACGAGATattcagaatcGTCTCGTGGGCTCGG
>Illumina UD IDT Index 2 (i5) Adapter UDP0149
@@ -981,6 +1091,10 @@ AATGATACGGCGACCACCGAGATCTACACcgccttctgaTCGTCGGCAGCGTC
CAAGCAGAAGACGGCATACGAGATattccgctatGTCTCGTGGGCTCGG
>Illumina UD IDT Index 2 (i5) Adapter UDP0155
AATGATACGGCGACCACCGAGATCTACACgcgcagagtaTCGTCGGCAGCGTC
+>Illumina UD IDT Index 1 (i7) Adapter UDP0155V3
+CAAGCAGAAGACGGCATACGAGATaatacgacatGTCTCGTGGGCTCGG
+>Illumina UD IDT Index 2 (i5) Adapter UDP0155V3
+AATGATACGGCGACCACCGAGATCTACACttcttgctggTCGTCGGCAGCGTC
>Illumina UD IDT Index 1 (i7) Adapter UDP0156
CAAGCAGAAGACGGCATACGAGATtgaatattgcGTCTCGTGGGCTCGG
>Illumina UD IDT Index 2 (i5) Adapter UDP0156
@@ -1077,6 +1191,10 @@ AATGATACGGCGACCACCGAGATCTACACctggatatgtTCGTCGGCAGCGTC
CAAGCAGAAGACGGCATACGAGATgcctcggataGTCTCGTGGGCTCGG
>Illumina UD IDT Index 2 (i5) Adapter UDP0179
AATGATACGGCGACCACCGAGATCTACACggccaataagTCGTCGGCAGCGTC
+>Illumina UD IDT Index 1 (i7) Adapter UDP0179V3
+CAAGCAGAAGACGGCATACGAGATgacaggtcggGTCTCGTGGGCTCGG
+>Illumina UD IDT Index 2 (i5) Adapter UDP0179V3
+AATGATACGGCGACCACCGAGATCTACACtgctcataacTCGTCGGCAGCGTC
>Illumina UD IDT Index 1 (i7) Adapter UDP0180
CAAGCAGAAGACGGCATACGAGATtgagacagcgGTCTCGTGGGCTCGG
>Illumina UD IDT Index 2 (i5) Adapter UDP0180
@@ -1133,18 +1251,34 @@ AATGATACGGCGACCACCGAGATCTACACgagttgtactTCGTCGGCAGCGTC
CAAGCAGAAGACGGCATACGAGATtatcatgagaGTCTCGTGGGCTCGG
>Illumina UD IDT Index 2 (i5) Adapter UDP0193
AATGATACGGCGACCACCGAGATCTACACaacacgtggaTCGTCGGCAGCGTC
+>Illumina UD IDT Index 1 (i7) Adapter UDP0193V3
+CAAGCAGAAGACGGCATACGAGATccgtaacgatGTCTCGTGGGCTCGG
+>Illumina UD IDT Index 2 (i5) Adapter UDP0193V3
+AATGATACGGCGACCACCGAGATCTACACgctccggaagTCGTCGGCAGCGTC
>Illumina UD IDT Index 1 (i7) Adapter UDP0194
CAAGCAGAAGACGGCATACGAGATcttggcctcgGTCTCGTGGGCTCGG
>Illumina UD IDT Index 2 (i5) Adapter UDP0194
AATGATACGGCGACCACCGAGATCTACACgtgttaccggTCGTCGGCAGCGTC
+>Illumina UD IDT Index 1 (i7) Adapter UDP0194V3
+CAAGCAGAAGACGGCATACGAGATtgacgtaggaGTCTCGTGGGCTCGG
+>Illumina UD IDT Index 2 (i5) Adapter UDP0194V3
+AATGATACGGCGACCACCGAGATCTACACtacttaagtgTCGTCGGCAGCGTC
>Illumina UD IDT Index 1 (i7) Adapter UDP0195
CAAGCAGAAGACGGCATACGAGATgtctcgtgaaGTCTCGTGGGCTCGG
>Illumina UD IDT Index 2 (i5) Adapter UDP0195
AATGATACGGCGACCACCGAGATCTACACagattgttacTCGTCGGCAGCGTC
+>Illumina UD IDT Index 1 (i7) Adapter UDP0195V3
+CAAGCAGAAGACGGCATACGAGATgcgatataacGTCTCGTGGGCTCGG
+>Illumina UD IDT Index 2 (i5) Adapter UDP0195V3
+AATGATACGGCGACCACCGAGATCTACACaagacaaggaTCGTCGGCAGCGTC
>Illumina UD IDT Index 1 (i7) Adapter UDP0196
CAAGCAGAAGACGGCATACGAGATccatccacgcGTCTCGTGGGCTCGG
>Illumina UD IDT Index 2 (i5) Adapter UDP0196
AATGATACGGCGACCACCGAGATCTACACttgaccaatgTCGTCGGCAGCGTC
+>Illumina UD IDT Index 1 (i7) Adapter UDP0196V3
+CAAGCAGAAGACGGCATACGAGATgatggccaacGTCTCGTGGGCTCGG
+>Illumina UD IDT Index 2 (i5) Adapter UDP0196V3
+AATGATACGGCGACCACCGAGATCTACACtgacattcgtTCGTCGGCAGCGTC
>Illumina UD IDT Index 1 (i7) Adapter UDP0197
CAAGCAGAAGACGGCATACGAGATacaaccaggaGTCTCGTGGGCTCGG
>Illumina UD IDT Index 2 (i5) Adapter UDP0197
@@ -1233,6 +1367,10 @@ AATGATACGGCGACCACCGAGATCTACACtcagttaatgTCGTCGGCAGCGTC
CAAGCAGAAGACGGCATACGAGATaatagagcaaGTCTCGTGGGCTCGG
>Illumina UD IDT Index 2 (i5) Adapter UDP0218
AATGATACGGCGACCACCGAGATCTACACgtgaccttgaTCGTCGGCAGCGTC
+>Illumina UD IDT Index 1 (i7) Adapter UDP0218V3
+CAAGCAGAAGACGGCATACGAGATtacgtagatgGTCTCGTGGGCTCGG
+>Illumina UD IDT Index 2 (i5) Adapter UDP0218V3
+AATGATACGGCGACCACCGAGATCTACACtgtaattgagTCGTCGGCAGCGTC
>Illumina UD IDT Index 1 (i7) Adapter UDP0219
CAAGCAGAAGACGGCATACGAGATctaactgtaaGTCTCGTGGGCTCGG
>Illumina UD IDT Index 2 (i5) Adapter UDP0219
@@ -1245,18 +1383,34 @@ AATGATACGGCGACCACCGAGATCTACACaacatacctaTCGTCGGCAGCGTC
CAAGCAGAAGACGGCATACGAGATtaccgaactaGTCTCGTGGGCTCGG
>Illumina UD IDT Index 2 (i5) Adapter UDP0221
AATGATACGGCGACCACCGAGATCTACACccatgtgtagTCGTCGGCAGCGTC
+>Illumina UD IDT Index 1 (i7) Adapter UDP0221V3
+CAAGCAGAAGACGGCATACGAGATtgcgctctagGTCTCGTGGGCTCGG
+>Illumina UD IDT Index 2 (i5) Adapter UDP0221V3
+AATGATACGGCGACCACCGAGATCTACACgcttctagcaTCGTCGGCAGCGTC
>Illumina UD IDT Index 1 (i7) Adapter UDP0222
CAAGCAGAAGACGGCATACGAGATgtagtaatagGTCTCGTGGGCTCGG
>Illumina UD IDT Index 2 (i5) Adapter UDP0222
AATGATACGGCGACCACCGAGATCTACACgagtctctccTCGTCGGCAGCGTC
+>Illumina UD IDT Index 1 (i7) Adapter UDP0222V3
+CAAGCAGAAGACGGCATACGAGATgcgtgatcgaGTCTCGTGGGCTCGG
+>Illumina UD IDT Index 2 (i5) Adapter UDP0222V3
+AATGATACGGCGACCACCGAGATCTACACcatagagcctTCGTCGGCAGCGTC
>Illumina UD IDT Index 1 (i7) Adapter UDP0223
CAAGCAGAAGACGGCATACGAGATggttatgctaGTCTCGTGGGCTCGG
>Illumina UD IDT Index 2 (i5) Adapter UDP0223
AATGATACGGCGACCACCGAGATCTACACgctatgcgcaTCGTCGGCAGCGTC
+>Illumina UD IDT Index 1 (i7) Adapter UDP0223V3
+CAAGCAGAAGACGGCATACGAGATgagccaggttGTCTCGTGGGCTCGG
+>Illumina UD IDT Index 2 (i5) Adapter UDP0223V3
+AATGATACGGCGACCACCGAGATCTACACtgagtatgttTCGTCGGCAGCGTC
>Illumina UD IDT Index 1 (i7) Adapter UDP0224
CAAGCAGAAGACGGCATACGAGATacaatagagtGTCTCGTGGGCTCGG
>Illumina UD IDT Index 2 (i5) Adapter UDP0224
AATGATACGGCGACCACCGAGATCTACACatcgcatatgTCGTCGGCAGCGTC
+>Illumina UD IDT Index 1 (i7) Adapter UDP0224V3
+CAAGCAGAAGACGGCATACGAGATacttccataaGTCTCGTGGGCTCGG
+>Illumina UD IDT Index 2 (i5) Adapter UDP0224V3
+AATGATACGGCGACCACCGAGATCTACACgacaataacaTCGTCGGCAGCGTC
>Illumina UD IDT Index 1 (i7) Adapter UDP0225
CAAGCAGAAGACGGCATACGAGATgcttccactaGTCTCGTGGGCTCGG
>Illumina UD IDT Index 2 (i5) Adapter UDP0225
@@ -1269,6 +1423,10 @@ AATGATACGGCGACCACCGAGATCTACACgaccggagatTCGTCGGCAGCGTC
CAAGCAGAAGACGGCATACGAGATaatatgaagcGTCTCGTGGGCTCGG
>Illumina UD IDT Index 2 (i5) Adapter UDP0227
AATGATACGGCGACCACCGAGATCTACACcgttcagcctTCGTCGGCAGCGTC
+>Illumina UD IDT Index 1 (i7) Adapter UDP0227V3
+CAAGCAGAAGACGGCATACGAGATttgaggctgcGTCTCGTGGGCTCGG
+>Illumina UD IDT Index 2 (i5) Adapter UDP0227V3
+AATGATACGGCGACCACCGAGATCTACACtaagtgctagTCGTCGGCAGCGTC
>Illumina UD IDT Index 1 (i7) Adapter UDP0228
CAAGCAGAAGACGGCATACGAGATtagcgctagtGTCTCGTGGGCTCGG
>Illumina UD IDT Index 2 (i5) Adapter UDP0228
@@ -1329,6 +1487,10 @@ AATGATACGGCGACCACCGAGATCTACACcttcgaaggaTCGTCGGCAGCGTC
CAAGCAGAAGACGGCATACGAGATaggttgcaggGTCTCGTGGGCTCGG
>Illumina UD IDT Index 2 (i5) Adapter UDP0242
AATGATACGGCGACCACCGAGATCTACACgtagagtcagTCGTCGGCAGCGTC
+>Illumina UD IDT Index 1 (i7) Adapter UDP0242
+CAAGCAGAAGACGGCATACGAGATagactctcttGTCTCGTGGGCTCGG
+>Illumina UD IDT Index 2 (i5) Adapter UDP0242
+AATGATACGGCGACCACCGAGATCTACACtacgaatcttTCGTCGGCAGCGTC
>Illumina UD IDT Index 1 (i7) Adapter UDP0243
CAAGCAGAAGACGGCATACGAGATgaaccatgaaGTCTCGTGGGCTCGG
>Illumina UD IDT Index 2 (i5) Adapter UDP0243
@@ -1337,6 +1499,10 @@ AATGATACGGCGACCACCGAGATCTACACgacattgtcaTCGTCGGCAGCGTC
CAAGCAGAAGACGGCATACGAGATttgagaggatGTCTCGTGGGCTCGG
>Illumina UD IDT Index 2 (i5) Adapter UDP0244
AATGATACGGCGACCACCGAGATCTACACtccgcaaggcTCGTCGGCAGCGTC
+>Illumina UD IDT Index 1 (i7) Adapter UDP0244
+CAAGCAGAAGACGGCATACGAGATtagccgagagGTCTCGTGGGCTCGG
+>Illumina UD IDT Index 2 (i5) Adapter UDP0244
+AATGATACGGCGACCACCGAGATCTACACtaccagatctTCGTCGGCAGCGTC
>Illumina UD IDT Index 1 (i7) Adapter UDP0245
CAAGCAGAAGACGGCATACGAGATtggtctagtgGTCTCGTGGGCTCGG
>Illumina UD IDT Index 2 (i5) Adapter UDP0245
@@ -1385,6 +1551,10 @@ AATGATACGGCGACCACCGAGATCTACACcacggattatTCGTCGGCAGCGTC
CAAGCAGAAGACGGCATACGAGATttatcttgcaGTCTCGTGGGCTCGG
>Illumina UD IDT Index 2 (i5) Adapter UDP0256
AATGATACGGCGACCACCGAGATCTACACttgaggacggTCGTCGGCAGCGTC
+>Illumina UD IDT Index 1 (i7) Adapter UDP0256V3
+CAAGCAGAAGACGGCATACGAGATtgttctatacGTCTCGTGGGCTCGG
+>Illumina UD IDT Index 2 (i5) Adapter UDP0256V3
+AATGATACGGCGACCACCGAGATCTACACtgtcacaggaTCGTCGGCAGCGTC
>Illumina UD IDT Index 1 (i7) Adapter UDP0257
CAAGCAGAAGACGGCATACGAGATagattgttacGTCTCGTGGGCTCGG
>Illumina UD IDT Index 2 (i5) Adapter UDP0257
@@ -1421,18 +1591,34 @@ AATGATACGGCGACCACCGAGATCTACACccacctgtgtTCGTCGGCAGCGTC
CAAGCAGAAGACGGCATACGAGATcgaggcggtaGTCTCGTGGGCTCGG
>Illumina UD IDT Index 2 (i5) Adapter UDP0265
AATGATACGGCGACCACCGAGATCTACACcctcgcaaccTCGTCGGCAGCGTC
+>Illumina UD IDT Index 1 (i7) Adapter UDP0265V3
+CAAGCAGAAGACGGCATACGAGATtctcggttagGTCTCGTGGGCTCGG
+>Illumina UD IDT Index 2 (i5) Adapter UDP0265V3
+AATGATACGGCGACCACCGAGATCTACACtcgatgcgcgTCGTCGGCAGCGTC
>Illumina UD IDT Index 1 (i7) Adapter UDP0266
CAAGCAGAAGACGGCATACGAGATgatataacagGTCTCGTGGGCTCGG
>Illumina UD IDT Index 2 (i5) Adapter UDP0266
AATGATACGGCGACCACCGAGATCTACACgtatagctgtTCGTCGGCAGCGTC
+>Illumina UD IDT Index 1 (i7) Adapter UDP0266V3
+CAAGCAGAAGACGGCATACGAGATcctagacactGTCTCGTGGGCTCGG
+>Illumina UD IDT Index 2 (i5) Adapter UDP0266V3
+AATGATACGGCGACCACCGAGATCTACACcctagaagcaTCGTCGGCAGCGTC
>Illumina UD IDT Index 1 (i7) Adapter UDP0267
CAAGCAGAAGACGGCATACGAGATtcgccggttaGTCTCGTGGGCTCGG
>Illumina UD IDT Index 2 (i5) Adapter UDP0267
AATGATACGGCGACCACCGAGATCTACACgctacattagTCGTCGGCAGCGTC
+>Illumina UD IDT Index 1 (i7) Adapter UDP0267V3
+CAAGCAGAAGACGGCATACGAGATgaagctcctcGTCTCGTGGGCTCGG
+>Illumina UD IDT Index 2 (i5) Adapter UDP0267V3
+AATGATACGGCGACCACCGAGATCTACACgacgtatacaTCGTCGGCAGCGTC
>Illumina UD IDT Index 1 (i7) Adapter UDP0268
CAAGCAGAAGACGGCATACGAGATagactctcttGTCTCGTGGGCTCGG
>Illumina UD IDT Index 2 (i5) Adapter UDP0268
AATGATACGGCGACCACCGAGATCTACACtacgaatcttTCGTCGGCAGCGTC
+>Illumina UD IDT Index 1 (i7) Adapter UDP0268V3
+CAAGCAGAAGACGGCATACGAGATtagtagatgaGTCTCGTGGGCTCGG
+>Illumina UD IDT Index 2 (i5) Adapter UDP0268V3
+AATGATACGGCGACCACCGAGATCTACACtaggcgacttTCGTCGGCAGCGTC
>Illumina UD IDT Index 1 (i7) Adapter UDP0269
CAAGCAGAAGACGGCATACGAGATgctcgcctacGTCTCGTGGGCTCGG
>Illumina UD IDT Index 2 (i5) Adapter UDP0269
@@ -1501,18 +1687,34 @@ AATGATACGGCGACCACCGAGATCTACACacggaatgcgTCGTCGGCAGCGTC
CAAGCAGAAGACGGCATACGAGATctcgttatcaGTCTCGTGGGCTCGG
>Illumina UD IDT Index 2 (i5) Adapter UDP0285
AATGATACGGCGACCACCGAGATCTACACgttccgcaggTCGTCGGCAGCGTC
+>Illumina UD IDT Index 1 (i7) Adapter UDP0285V3
+CAAGCAGAAGACGGCATACGAGATgatgccaaggGTCTCGTGGGCTCGG
+>Illumina UD IDT Index 2 (i5) Adapter UDP0285V3
+AATGATACGGCGACCACCGAGATCTACACgaccgattcgTCGTCGGCAGCGTC
>Illumina UD IDT Index 1 (i7) Adapter UDP0286
CAAGCAGAAGACGGCATACGAGATccttactatgGTCTCGTGGGCTCGG
>Illumina UD IDT Index 2 (i5) Adapter UDP0286
AATGATACGGCGACCACCGAGATCTACACaccaagttacTCGTCGGCAGCGTC
+>Illumina UD IDT Index 1 (i7) Adapter UDP0286V3
+CAAGCAGAAGACGGCATACGAGATagtacctataGTCTCGTGGGCTCGG
+>Illumina UD IDT Index 2 (i5) Adapter UDP0286V3
+AATGATACGGCGACCACCGAGATCTACACtaggtgagatTCGTCGGCAGCGTC
>Illumina UD IDT Index 1 (i7) Adapter UDP0287
CAAGCAGAAGACGGCATACGAGATagaagccaatGTCTCGTGGGCTCGG
>Illumina UD IDT Index 2 (i5) Adapter UDP0287
AATGATACGGCGACCACCGAGATCTACACtggctcgcagTCGTCGGCAGCGTC
+>Illumina UD IDT Index 1 (i7) Adapter UDP0287V3
+CAAGCAGAAGACGGCATACGAGATtgtagacttgGTCTCGTGGGCTCGG
+>Illumina UD IDT Index 2 (i5) Adapter UDP0287V3
+AATGATACGGCGACCACCGAGATCTACACcacgtacgtgTCGTCGGCAGCGTC
>Illumina UD IDT Index 1 (i7) Adapter UDP0288
CAAGCAGAAGACGGCATACGAGATtaatcggtacGTCTCGTGGGCTCGG
>Illumina UD IDT Index 2 (i5) Adapter UDP0288
AATGATACGGCGACCACCGAGATCTACACaactaacgttTCGTCGGCAGCGTC
+>Illumina UD IDT Index 1 (i7) Adapter UDP0288V3
+CAAGCAGAAGACGGCATACGAGATtcctcttctcGTCTCGTGGGCTCGG
+>Illumina UD IDT Index 2 (i5) Adapter UDP0288V3
+AATGATACGGCGACCACCGAGATCTACACttgacctaacTCGTCGGCAGCGTC
>Illumina UD IDT Index 1 (i7) Adapter UDP0289V2
CAAGCAGAAGACGGCATACGAGATgctactatctGTCTCGTGGGCTCGG
>Illumina UD IDT Index 2 (i5) Adapter UDP0289V2
@@ -1553,6 +1755,10 @@ AATGATACGGCGACCACCGAGATCTACACactagaacttTCGTCGGCAGCGTC
CAAGCAGAAGACGGCATACGAGATctcgactcctGTCTCGTGGGCTCGG
>Illumina UD IDT Index 2 (i5) Adapter UDP0298
AATGATACGGCGACCACCGAGATCTACACttaggcttacTCGTCGGCAGCGTC
+>Illumina UD IDT Index 1 (i7) Adapter UDP0298V3
+CAAGCAGAAGACGGCATACGAGATgataacctggGTCTCGTGGGCTCGG
+>Illumina UD IDT Index 2 (i5) Adapter UDP0298V3
+AATGATACGGCGACCACCGAGATCTACACgaatgcagttTCGTCGGCAGCGTC
>Illumina UD IDT Index 1 (i7) Adapter UDP0299
CAAGCAGAAGACGGCATACGAGATagtgagtgaaGTCTCGTGGGCTCGG
>Illumina UD IDT Index 2 (i5) Adapter UDP0299
@@ -1645,6 +1851,10 @@ AATGATACGGCGACCACCGAGATCTACACctaggcaaggTCGTCGGCAGCGTC
CAAGCAGAAGACGGCATACGAGATctagcgtcgaGTCTCGTGGGCTCGG
>Illumina UD IDT Index 2 (i5) Adapter UDP0321
AATGATACGGCGACCACCGAGATCTACACcctcttcgaaTCGTCGGCAGCGTC
+>Illumina UD IDT Index 1 (i7) Adapter UDP0321V3
+CAAGCAGAAGACGGCATACGAGATgcggagttacGTCTCGTGGGCTCGG
+>Illumina UD IDT Index 2 (i5) Adapter UDP0321V3
+AATGATACGGCGACCACCGAGATCTACACaatagaacggTCGTCGGCAGCGTC
>Illumina UD IDT Index 1 (i7) Adapter UDP0322
CAAGCAGAAGACGGCATACGAGATtgcctacgagGTCTCGTGGGCTCGG
>Illumina UD IDT Index 2 (i5) Adapter UDP0322
@@ -1837,18 +2047,34 @@ AATGATACGGCGACCACCGAGATCTACACgccagatccaTCGTCGGCAGCGTC
CAAGCAGAAGACGGCATACGAGATgttatatggcGTCTCGTGGGCTCGG
>Illumina UD IDT Index 2 (i5) Adapter UDP0369
AATGATACGGCGACCACCGAGATCTACACacacaatatcTCGTCGGCAGCGTC
+>Illumina UD IDT Index 1 (i7) Adapter UDP0369V3
+CAAGCAGAAGACGGCATACGAGATtgaattcatcGTCTCGTGGGCTCGG
+>Illumina UD IDT Index 2 (i5) Adapter UDP0369V3
+AATGATACGGCGACCACCGAGATCTACACtgctgtgattTCGTCGGCAGCGTC
>Illumina UD IDT Index 1 (i7) Adapter UDP0370
CAAGCAGAAGACGGCATACGAGATcactcgcactGTCTCGTGGGCTCGG
>Illumina UD IDT Index 2 (i5) Adapter UDP0370
AATGATACGGCGACCACCGAGATCTACACtggaggtaatTCGTCGGCAGCGTC
+>Illumina UD IDT Index 1 (i7) Adapter UDP0370V3
+CAAGCAGAAGACGGCATACGAGATtgctgtgattGTCTCGTGGGCTCGG
+>Illumina UD IDT Index 2 (i5) Adapter UDP0370V3
+AATGATACGGCGACCACCGAGATCTACACgatcgaataaTCGTCGGCAGCGTC
>Illumina UD IDT Index 1 (i7) Adapter UDP0371
CAAGCAGAAGACGGCATACGAGATaccggctcagGTCTCGTGGGCTCGG
>Illumina UD IDT Index 2 (i5) Adapter UDP0371
AATGATACGGCGACCACCGAGATCTACACccttcacgtaTCGTCGGCAGCGTC
+>Illumina UD IDT Index 1 (i7) Adapter UDP0371V3
+CAAGCAGAAGACGGCATACGAGATcatggttcgtGTCTCGTGGGCTCGG
+>Illumina UD IDT Index 2 (i5) Adapter UDP0371V3
+AATGATACGGCGACCACCGAGATCTACACactgaattacTCGTCGGCAGCGTC
>Illumina UD IDT Index 1 (i7) Adapter UDP0372
CAAGCAGAAGACGGCATACGAGATatagaccgttGTCTCGTGGGCTCGG
>Illumina UD IDT Index 2 (i5) Adapter UDP0372
AATGATACGGCGACCACCGAGATCTACACctatacgcggTCGTCGGCAGCGTC
+>Illumina UD IDT Index 1 (i7) Adapter UDP0372V3
+CAAGCAGAAGACGGCATACGAGATtacttggttgGTCTCGTGGGCTCGG
+>Illumina UD IDT Index 2 (i5) Adapter UDP0372V3
+AATGATACGGCGACCACCGAGATCTACACccatccacgcTCGTCGGCAGCGTC
>Illumina UD IDT Index 1 (i7) Adapter UDP0373
CAAGCAGAAGACGGCATACGAGATtgaacgcaacGTCTCGTGGGCTCGG
>Illumina UD IDT Index 2 (i5) Adapter UDP0373
@@ -2801,9 +3027,10 @@ EOF
# ============ #
# #
mandoc() {
- echo -e "\n\033[1m fqCleanER v$VERSION $COPYRIGHT\033[0m";
+ echo -e "\n\033[1m fqCleanER v$VERSION $COPYRIGHT\033[0m";
cat <<EOF
+ https://research.pasteur.fr/en/tool/fqcleaner
https://gitlab.pasteur.fr/GIPhy/fqCleanER
USAGE: fqCleanER.sh [options]
@@ -3588,7 +3815,7 @@ fqmerge() {
## PE lib 3
if [ "$I31,$I32" != "$NA2" ]
then
- [ "$I3M" != "$Na" ] && cp $I3M $O3M || touch $O3M ;
+ [ "$I3M" != "$NA" ] && cp $I3M $O3M || touch $O3M ;
local rb="$(fqsize $I31 $I32)"; local arl=$(( $(get "$rb" 2) / $(get "$rb" 1) )); ## rl = avg read lgt
$FLASH -M $(bc -l <<<"scale=0;($arl*$M_SCALE_FLASH+0.5)/1") -t $4 -d $(dirname $b3p) -o $(basename $b3p) $I31 $I32 &>/dev/null ;
mv $b3p.notCombined_1.fastq $O31 ;
@@ -3882,7 +4109,7 @@ FQ5S="$NA"; # lib5 SE file -8
FQ6S="$NA"; # lib6 SE file -9
OUTDIR="$NA"; # outdir -o
BASENAME="$NA"; # basename -b
-TMPDIR=${TMPDIR:-/tmp}; # tmp directory -w
+TMP_DIR=${TMPDIR:-/tmp}; # tmp directory -w
ALIENS="$NA"; # alien oligo -a
CONTA="$NA"; # contaminant file -A
STEPS="$NA"; # processing step(s) -s
@@ -3919,7 +4146,7 @@ do
c) MINCOV=$OPTARG ;;
C) MAXCOV=$OPTARG ;;
t) NTHREADS=$OPTARG ;;
- w) TMPDIR="$OPTARG" ;;
+ w) TMP_DIR="$OPTARG" ;;
z) ZIP="$OPTARG" ;;
h) mandoc ; exit 0 ;;
\?) mandoc ; exit 1 ;;
@@ -3985,7 +4212,7 @@ then
LIB3=true;
echo "> PE lib 3" ;
echo -e "+ FQ31: $(disp $FQ31)";
- echo -e "+ FQ32: $(disp $FQ31)";
+ echo -e "+ FQ32: $(disp $FQ32)";
fi
## SE lib 4 #################################################################################################
if [ "$FQ4S" != "$NA" ]
@@ -4035,10 +4262,10 @@ if [ $MINCOV -ge $MAXCOV ]; then echo "min too large (options -c/-C): $
## NTHREADS #################################################################################################
if ! [[ $NTHREADS =~ ^[0-9]+$ ]]; then echo "incorrect value: $NTHREADS (option -t)" >&2 ; exit 1 ; fi
## TMPDIR ###################################################################################################
-[ "${TMPDIR:0:1}" != "/" ] && TMPDIR="$(pwd)/$TMPDIR";
-if [ ! -e $TMPDIR ]; then echo "tmp directory does not exist (option -w): $TMPDIR" >&2 ; exit 1 ; fi
-if [ ! -d $TMPDIR ]; then echo "not a directory (option -w): $TMPDIR" >&2 ; exit 1 ; fi
-if [ ! -w $TMPDIR ]; then echo "no write permission (option -w): $TMPDIR" >&2 ; exit 1 ; fi
+[ "${TMP_DIR:0:1}" != "/" ] && TMP_DIR="$(pwd)/$TMP_DIR";
+if [ ! -e $TMP_DIR ]; then echo "tmp directory does not exist (option -w): $TMPDIR" >&2 ; exit 1 ; fi
+if [ ! -d $TMP_DIR ]; then echo "not a directory (option -w): $TMPDIR" >&2 ; exit 1 ; fi
+if [ ! -w $TMP_DIR ]; then echo "no write permission (option -w): $TMPDIR" >&2 ; exit 1 ; fi
## BASENAME #################################################################################################
if [ "$BASENAME" == "$NA" ]; then echo "basename not specified (option -b)" >&2 ; exit 1 ; fi
## OUTDIR ###################################################################################################
@@ -4068,12 +4295,30 @@ fi
echo "# output directory" ; echo "+ OUTDIR=$OUTDIR" ;
## TMPDIR ###################################################################################################
-TMP_DIR=$(mktemp -d -p $TMPDIR -t fqCleanER.$BASENAME.XXXXXXXXX);
+TMP_DIR=$(mktemp -d -p $TMP_DIR fqCleanER.$BASENAME.XXXXXXXXX);
echo "# tmp directory" ; echo "+ TMP_DIR=$TMP_DIR" ;
## SYSTEM SPEC ##############################################################################################
export LC_ALL=C ;
-trap "echo -n interrupting ; echo -n . ; kill -9 $(jobs -pr) &> /dev/null ; echo -n . ; wait ; echo -n . ; rm -rf $TMP_DIR/* &>/dev/null ; wait ; echo -n . ; rm -rf $TMP_DIR &>/dev/null ; while [ -e $TMP_DIR ]; do sleep 1 ; echo -n . ; rm -rf $TMP_DIR &>/dev/null ; done ; echo ; exit " SIGINT
+arf() {
+ echo -n " [stop] >>" >&2 ;
+ sleep 1 ;
+ echo -n " [kill jobs] >>" >&2 ;
+ kill -9 $(jobs -pr) &> /dev/null ;
+ sleep 1 ;
+ echo -n ">>" >&2 ;
+ wait ;
+ echo -n " [rm tmp dir] >" >&2 ;
+ while [ -e $TMP_DIR ]
+ do
+ rm -rf $TMP_DIR &>/dev/null ;
+ echo -n ">" >&2 ;
+ sleep 1 ;
+ done
+ echo " [exit]" >&2 ;
+}
+trap 'arf;exit 1' SIGTERM SIGINT SIGQUIT SIGHUP TERM INT QUIT HUP ; # &> /dev/null ;
+
## TMP FILES ################################################################################################
# PE lib 1