Skip to content
GitLab
Menu
Projects
Groups
Snippets
/
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
Amine GHOZLANE
shaman
Commits
8e65da7d
Commit
8e65da7d
authored
Apr 21, 2017
by
svolant
Browse files
correction bug
parents
db6ccd7c
be3c3d82
Changes
4
Hide whitespace changes
Inline
Side-by-side
.gitignore
View file @
8e65da7d
...
...
@@ -3,5 +3,4 @@
*.RData
.Rproj.user
*.Rproj
AideCode.odt
www/google-analytics.js
*.json
LoadPackages.R
View file @
8e65da7d
options
(
download.file.method
=
'wget'
)
if
(
!
require
(
"backports"
)){
install.packages
(
"backports"
)
library
(
backports
)
}
if
(
!
require
(
"backports"
)){
install.packages
(
"backports"
)
...
...
@@ -8,15 +12,18 @@ if (!require("backports")){
if
(
!
require
(
"readr"
)){
install.packages
(
"readr"
)
library
(
readr
)
}
if
(
!
require
(
"jsonlite"
)){
install.packages
(
"jsonlite"
)
library
(
jsonlite
)
}
if
(
!
require
(
"shinyFiles"
)){
install.packages
(
"shinyFiles"
)
library
(
shinyFiles
)
}
...
...
@@ -179,6 +186,7 @@ if(!require(PhyloTreeMetaR)){
library
(
PhyloTreeMetaR
)
}
# if(!require(plotly)){
# install.packages("plotly")
# library(plotly)
...
...
Rfunctions/Data_Management.R
View file @
8e65da7d
...
...
@@ -317,8 +317,7 @@ SamplesMasque <- function(input,values)
CreateJSON
<-
function
(
input
){
curdir
=
getwd
()
curdir
<-
getwd
()
tmpjson
=
tempfile
(
pattern
=
"file"
,
tmpdir
=
paste
(
curdir
,
"www"
,
"masque"
,
"todo"
,
sep
=
.Platform
$
file.sep
),
fileext
=
".json"
)
if
(
input
$
PairedOrNot
==
'n'
)
...
...
www/alienTrimmerPF8contaminants.fasta
0 → 100644
View file @
8e65da7d
####################################################################################################
# #
# LAST UPDATE: 07 June 2013 #
# #
# This file contains a list a putative contaminant oligonucleotides that could occur in both ends #
# of NGS reads. This file is formatted to be used by AlienTrimmer in order to trim off such #
# contaminant oligonucleotides from FASTQ formatted read files. #
# If you wish to add new contaminant sequences, use the FASTA format to name them, and be careful #
# to always write one sequence per line (lower and/or uppercase characters). Comment lines could #
# be written by using '#' as the first character. If you wish to not trim off some of these #
# sequences when using AlienTrimmer, comment these lines with '#'. #
# #
# CONTENTS: #
# 1. Homopolymers #
# 2. Nextera DNA Sample Preparation Kit (Illumina) #
# 3. Nextera Index Kit- PCR Primers #
# 4. Nextera DNA Sample Prep Kit (Epicentre Biotechnologies) #
# 5. TruSeq RNA and DNA Sample Prep Kits (v1 and v2) #
# 6. Oligonucleotide sequences for TruSeq Small RNA Sample Prep Kit #
# 7. Illumina oligonucleotide sequences for Genomic DNA #
# 8. Illumina Paired End DNA oligonucleotide sequences #
# 9. Illumina Oligonucleotide sequences for the Multiplexing Sample Prep Oligo Only Kit #
# 10. Illumina DpnII expression #
# 11. Illumina DpnII Gex #
# 12. Illumina NlaIII expression #
# 13. Illumina Small RNA Kits v1 and v1.5 #
# 14. SOLID 3 System Oligo #
# 15. Roche 454 Adaptors, Linkiers and Adapters #
# 16. Ion Torrent adapter sequences #
# #
####################################################################################################
###################################################################################################
### 1. Homopolymers ###############################################################################
###################################################################################################
>poly-A
AAAAAAAAAAAAAAAAAAAA
>poly-C
CCCCCCCCCCCCCCCCCCCC
>poly-G
GGGGGGGGGGGGGGGGGGGG
>poly-T
TTTTTTTTTTTTTTTTTTTT
###################################################################################################
### 2. Nextera(R) DNA Sample Preparation Kit (Illumina) ###########################################
###################################################################################################
>Nextera Transposase Sequence (FC-121-1031)
TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG
>Nextera Transposase Sequence (FC-121-1030)
GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG
###################################################################################################
### 3. Nextera Index Kit- PCR Primers #############################################################
###################################################################################################
>Nextera Index Kit- PCR primer (FC-121-1012, Index N501)
AATGATACGGCGACCACCGAGATCTACACtagatcgcTCGTCGGCAGCGTC
>Nextera Index Kit- PCR primer (FC-121-1012, Index N502)
AATGATACGGCGACCACCGAGATCTACACctctctatTCGTCGGCAGCGTC
>Nextera Index Kit- PCR primer (FC-121-1012, Index N503)
AATGATACGGCGACCACCGAGATCTACACtatcctctTCGTCGGCAGCGTC
>Nextera Index Kit- PCR primer (FC-121-1012, Index N504)
AATGATACGGCGACCACCGAGATCTACACagagtagaTCGTCGGCAGCGTC
>Nextera Index Kit- PCR primer (FC-121-1012, Index N505)
AATGATACGGCGACCACCGAGATCTACACgtaaggagTCGTCGGCAGCGTC
>Nextera Index Kit- PCR primer (FC-121-1012, Index N506)
AATGATACGGCGACCACCGAGATCTACACgctgcataTCGTCGGCAGCGTC
>Nextera Index Kit- PCR primer (FC-121-1012, Index N507)
AATGATACGGCGACCACCGAGATCTACACaaggagtaTCGTCGGCAGCGTC
>Nextera Index Kit- PCR primer (FC-121-1012, Index N508)
AATGATACGGCGACCACCGAGATCTACACctaagcctTCGTCGGCAGCGTC
>Nextera Index Kit- PCR primer (FC-121-1011, Index N701)
CAAGCAGAAGACGGCATACGAGATtaaggcgaGTCTCGTGGGCTCGG
>Nextera Index Kit- PCR primer (FC-121-1011, Index N702)
CAAGCAGAAGACGGCATACGAGATcgtactagGTCTCGTGGGCTCGG
>Nextera Index Kit- PCR primer (FC-121-1011, Index N703)
CAAGCAGAAGACGGCATACGAGATaggcagaaGTCTCGTGGGCTCGG
>Nextera Index Kit- PCR primer (FC-121-1011, Index N704)
CAAGCAGAAGACGGCATACGAGATtcctgagcGTCTCGTGGGCTCGG
>Nextera Index Kit- PCR primer (FC-121-1011, Index N705)
CAAGCAGAAGACGGCATACGAGATggactcctGTCTCGTGGGCTCGG
>Nextera Index Kit- PCR primer (FC-121-1011, Index N706)
CAAGCAGAAGACGGCATACGAGATtaggcatgGTCTCGTGGGCTCGG
>Nextera Index Kit- PCR primer (FC-121-1011, Index N707)
CAAGCAGAAGACGGCATACGAGATctctctacGTCTCGTGGGCTCGG
>Nextera Index Kit- PCR primer (FC-121-1011, Index N708)
CAAGCAGAAGACGGCATACGAGATcagagaggGTCTCGTGGGCTCGG
>Nextera Index Kit- PCR primer (FC-121-1011, Index N709)
CAAGCAGAAGACGGCATACGAGATgctacgctGTCTCGTGGGCTCGG
>Nextera Index Kit- PCR primer (FC-121-1011, Index N710)
CAAGCAGAAGACGGCATACGAGATcgaggctgGTCTCGTGGGCTCGG
>Nextera Index Kit- PCR primer (FC-121-1011, Index N711)
CAAGCAGAAGACGGCATACGAGATaagaggcaGTCTCGTGGGCTCGG
>Nextera Index Kit- PCR primer (FC-121-1011, Index N712)
CAAGCAGAAGACGGCATACGAGATgtagaggaGTCTCGTGGGCTCGG
#########################################################################################################
### 4. Nextera DNA Sample Prep Kit (Epicentre Biotechnologies) ##########################################
#########################################################################################################
>Transposon Sequence 1
GCCTCCCTCGCGCCATCAGAGATGTGTATAAGAGACAG
>Transposon Sequence 2
GCCTTGCCAGCCCGCTCAGAGATGTGTATAAGAGACAG
>Adapter 1
AATGATACGGCGACCACCGAGATCTACACGCCTCCCTCGCGCCATCAG
>Adapter 2, Bar Code IDX1
CAAGCAGAAGACGGCATACGAGATcgtgatCGGTCTGCCTTGCCAGCCCGCTCAG
>Adapter 2, Bar Code IDX2
CAAGCAGAAGACGGCATACGAGATacatcgCGGTCTGCCTTGCCAGCCCGCTCAG
>Adapter 2, Bar Code IDX3
CAAGCAGAAGACGGCATACGAGATgcctaaCGGTCTGCCTTGCCAGCCCGCTCAG
>Adapter 2, Bar Code IDX4
CAAGCAGAAGACGGCATACGAGATtggtcaCGGTCTGCCTTGCCAGCCCGCTCAG
>Adapter 2, Bar Code IDX5
CAAGCAGAAGACGGCATACGAGATcactgtCGGTCTGCCTTGCCAGCCCGCTCAG
>Adapter 2, Bar Code IDX6
CAAGCAGAAGACGGCATACGAGATattggcCGGTCTGCCTTGCCAGCCCGCTCAG
>Adapter 2, Bar Code IDX7
CAAGCAGAAGACGGCATACGAGATgatctgCGGTCTGCCTTGCCAGCCCGCTCAG
>Adapter 2, Bar Code IDX8
CAAGCAGAAGACGGCATACGAGATtcaagtCGGTCTGCCTTGCCAGCCCGCTCAG
>Adapter 2, Bar Code IDX9
CAAGCAGAAGACGGCATACGAGATctgatcCGGTCTGCCTTGCCAGCCCGCTCAG
>Adapter 2, Bar Code IDX10
CAAGCAGAAGACGGCATACGAGATaagctaCGGTCTGCCTTGCCAGCCCGCTCAG
>Adapter 2, Bar Code IDX11
CAAGCAGAAGACGGCATACGAGATgtagccCGGTCTGCCTTGCCAGCCCGCTCAG
>Adapter 2, Bar Code IDX12
CAAGCAGAAGACGGCATACGAGATtacaagCGGTCTGCCTTGCCAGCCCGCTCAG
>PCR Primer 1
AATGATACGGCGACCACCGA
>PCR Primer 2
CAAGCAGAAGACGGCATACGA
#########################################################################################################
### 5. TruSeq RNA and DNA Sample Prep Kits (v1 and v2) ##################################################
#########################################################################################################
>TruSeq Universal Adapter
AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
>TruSeq Adapter, Index 1
GATCGGAAGAGCACACGTCTGAACTCCAGTCACatcacgATCTCGTATGCCGTCTTCTGCTTG
>TruSeq Adapter, Index 2
GATCGGAAGAGCACACGTCTGAACTCCAGTCACcgatgtATCTCGTATGCCGTCTTCTGCTTG
>TruSeq Adapter, Index 3
GATCGGAAGAGCACACGTCTGAACTCCAGTCACttaggcATCTCGTATGCCGTCTTCTGCTTG
>TruSeq Adapter, Index 4
GATCGGAAGAGCACACGTCTGAACTCCAGTCACtgaccaATCTCGTATGCCGTCTTCTGCTTG
>TruSeq Adapter, Index 5
GATCGGAAGAGCACACGTCTGAACTCCAGTCACacagtgATCTCGTATGCCGTCTTCTGCTTG
>TruSeq Adapter, Index 6
GATCGGAAGAGCACACGTCTGAACTCCAGTCACgccaatATCTCGTATGCCGTCTTCTGCTTG
>TruSeq Adapter, Index 7
GATCGGAAGAGCACACGTCTGAACTCCAGTCACcagatcATCTCGTATGCCGTCTTCTGCTTG
>TruSeq Adapter, Index 8
GATCGGAAGAGCACACGTCTGAACTCCAGTCACacttgaATCTCGTATGCCGTCTTCTGCTTG
>TruSeq Adapter, Index 9
GATCGGAAGAGCACACGTCTGAACTCCAGTCACgatcagATCTCGTATGCCGTCTTCTGCTTG
>TruSeq Adapter, Index 10
GATCGGAAGAGCACACGTCTGAACTCCAGTCACtagcttATCTCGTATGCCGTCTTCTGCTTG
>TruSeq Adapter, Index 11
GATCGGAAGAGCACACGTCTGAACTCCAGTCACggctacATCTCGTATGCCGTCTTCTGCTTG
>TruSeq Adapter, Index 12
GATCGGAAGAGCACACGTCTGAACTCCAGTCACcttgtaATCTCGTATGCCGTCTTCTGCTTG
>TruSeq Adapter, Index 13
GATCGGAAGAGCACACGTCTGAACTCCAGTCACagtcaaCAATCTCGTATGCCGTCTTCTGCTTG
>TruSeq Adapter, Index 14
GATCGGAAGAGCACACGTCTGAACTCCAGTCACagttccGTATCTCGTATGCCGTCTTCTGCTTG
>TruSeq Adapter, Index 15
GATCGGAAGAGCACACGTCTGAACTCCAGTCACatgtcaGAATCTCGTATGCCGTCTTCTGCTTG
>TruSeq Adapter, Index 16
GATCGGAAGAGCACACGTCTGAACTCCAGTCACccgtccCGATCTCGTATGCCGTCTTCTGCTTG
>TruSeq Adapter, Index 18
GATCGGAAGAGCACACGTCTGAACTCCAGTCACgtccgcACATCTCGTATGCCGTCTTCTGCTTG
>TruSeq Adapter, Index 19
GATCGGAAGAGCACACGTCTGAACTCCAGTCACgtgaaaCGATCTCGTATGCCGTCTTCTGCTTG
>TruSeq Adapter, Index 20
GATCGGAAGAGCACACGTCTGAACTCCAGTCACgtggccTTATCTCGTATGCCGTCTTCTGCTTG
>TruSeq Adapter, Index 21
GATCGGAAGAGCACACGTCTGAACTCCAGTCACgtttcgGAATCTCGTATGCCGTCTTCTGCTTG
>TruSeq Adapter, Index 22
GATCGGAAGAGCACACGTCTGAACTCCAGTCACcgtacgTAATCTCGTATGCCGTCTTCTGCTTG
>TruSeq Adapter, Index 23
GATCGGAAGAGCACACGTCTGAACTCCAGTCACgagtggATATCTCGTATGCCGTCTTCTGCTTG
>TruSeq Adapter, Index 25
GATCGGAAGAGCACACGTCTGAACTCCAGTCACactgatATATCTCGTATGCCGTCTTCTGCTTG
>TruSeq Adapter, Index 27
GATCGGAAGAGCACACGTCTGAACTCCAGTCACattcctTTATCTCGTATGCCGTCTTCTGCTTG
#########################################################################################################
### 6. Oligonucleotide sequences for TruSeq Small RNA Sample Prep Kit ###################################
#########################################################################################################
>RNA 3’ Adapter (RA3), part # 15013207
TGGAATTCTCGGGTGCCAAGG
>RNA RT Primer (RTP), part # 15013981
GCCTTGGCACCCGAGAATTCCA
>RNA PCR Primer, (RP1), part # 15005505
AATGATACGGCGACCACCGAGATCTACACGTTCAGAGTTCTACAGTCCGA
>RNA PCR Primer, Index 1 (RPI1)
CAAGCAGAAGACGGCATACGAGATcgtgatGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
>RNA PCR Primer, Index 2 (RPI2)
CAAGCAGAAGACGGCATACGAGATacatcgGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
>RNA PCR Primer, Index 3 (RPI3)
CAAGCAGAAGACGGCATACGAGATgcctaaGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
>RNA PCR Primer, Index 4 (RPI4)
CAAGCAGAAGACGGCATACGAGATtggtcaGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
>RNA PCR Primer, Index 5 (RPI5)
CAAGCAGAAGACGGCATACGAGATcactgtGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
>RNA PCR Primer, Index 6 (RPI6)
CAAGCAGAAGACGGCATACGAGATattggcGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
>RNA PCR Primer, Index 7 (RPI7)
CAAGCAGAAGACGGCATACGAGATgatctgGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
>RNA PCR Primer, Index 8 (RPI8)
CAAGCAGAAGACGGCATACGAGATtcaagtGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
>RNA PCR Primer, Index 9 (RPI9)
CAAGCAGAAGACGGCATACGAGATctgatcGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
>RNA PCR Primer, Index 10 (RPI10)
CAAGCAGAAGACGGCATACGAGATaagctaGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
>RNA PCR Primer, Index 11 (RPI11)
CAAGCAGAAGACGGCATACGAGATgtagccGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
>RNA PCR Primer, Index 12 (RPI12)
CAAGCAGAAGACGGCATACGAGATtacaagGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
>RNA PCR Primer, Index 13 (RPI13)
CAAGCAGAAGACGGCATACGAGATttgactGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
>RNA PCR Primer, Index 14 (RPI14)
CAAGCAGAAGACGGCATACGAGATggaactGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
>RNA PCR Primer, Index 15 (RPI15)
CAAGCAGAAGACGGCATACGAGATtgacatGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
>RNA PCR Primer, Index 16 (RPI16)
CAAGCAGAAGACGGCATACGAGATggacggGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
>RNA PCR Primer, Index 17 (RPI17)
CAAGCAGAAGACGGCATACGAGATctctacGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
>RNA PCR Primer, Index 18 (RPI18)
CAAGCAGAAGACGGCATACGAGATgcggacGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
>RNA PCR Primer, Index 19 (RPI19)
CAAGCAGAAGACGGCATACGAGATtttcacGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
>RNA PCR Primer, Index 20 (RPI20)
CAAGCAGAAGACGGCATACGAGATggccacGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
>RNA PCR Primer, Index 21 (RPI21)
CAAGCAGAAGACGGCATACGAGATcgaaacGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
>RNA PCR Primer, Index 22 (RPI22)
CAAGCAGAAGACGGCATACGAGATcgtacgGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
>RNA PCR Primer, Index 23 (RPI23)
CAAGCAGAAGACGGCATACGAGATccactcGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
>RNA PCR Primer, Index 24 (RPI24)
CAAGCAGAAGACGGCATACGAGATgctaccGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
>RNA PCR Primer, Index 25 (RPI25)
CAAGCAGAAGACGGCATACGAGATatcagtGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
>RNA PCR Primer, Index 26 (RPI26)
CAAGCAGAAGACGGCATACGAGATgctcatGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
>RNA PCR Primer, Index 27 (RPI27)
CAAGCAGAAGACGGCATACGAGATaggaatGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
>RNA PCR Primer, Index 28 (RPI28)
CAAGCAGAAGACGGCATACGAGATcttttgGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
>RNA PCR Primer, Index 29 (RPI29)
CAAGCAGAAGACGGCATACGAGATtagttgGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
>RNA PCR Primer, Index 30 (RPI30)
CAAGCAGAAGACGGCATACGAGATccggtgGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
>RNA PCR Primer, Index 31 (RPI31)
CAAGCAGAAGACGGCATACGAGATatcgtgGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
>RNA PCR Primer, Index 32 (RPI32)
CAAGCAGAAGACGGCATACGAGATtgagtgGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
>RNA PCR Primer, Index 33 (RPI33)
CAAGCAGAAGACGGCATACGAGATcgcctgGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
>RNA PCR Primer, Index 34 (RPI34)
CAAGCAGAAGACGGCATACGAGATgccatgGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
>RNA PCR Primer, Index 35 (RPI35)
CAAGCAGAAGACGGCATACGAGATaaaatgGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
>RNA PCR Primer, Index 36 (RPI36)
CAAGCAGAAGACGGCATACGAGATtgttggGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
>RNA PCR Primer, Index 37 (RPI37)
CAAGCAGAAGACGGCATACGAGATattccgGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
>RNA PCR Primer, Index 38 (RPI38)
CAAGCAGAAGACGGCATACGAGATagctagGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
>RNA PCR Primer, Index 39 (RPI39)
CAAGCAGAAGACGGCATACGAGATgtatagGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
>RNA PCR Primer, Index 40 (RPI40)
CAAGCAGAAGACGGCATACGAGATtctgagGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
>RNA PCR Primer, Index 41 (RPI41)
CAAGCAGAAGACGGCATACGAGATgtcgtcGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
>RNA PCR Primer, Index 42 (RPI42)
CAAGCAGAAGACGGCATACGAGATcgattaGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
>RNA PCR Primer, Index 43 (RPI43)
CAAGCAGAAGACGGCATACGAGATgctgtaGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
>RNA PCR Primer, Index 44 (RPI44)
CAAGCAGAAGACGGCATACGAGATattataGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
>RNA PCR Primer, Index 45 (RPI45)
CAAGCAGAAGACGGCATACGAGATgaatgaGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
>RNA PCR Primer, Index 46 (RPI46)
CAAGCAGAAGACGGCATACGAGATtcgggaGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
>RNA PCR Primer, Index 47 (RPI47)
CAAGCAGAAGACGGCATACGAGATcttcgaGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
>RNA PCR Primer, Index 48 (RPI48)
CAAGCAGAAGACGGCATACGAGATtgccgaGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
#########################################################################################################
### 7. Illumina oligonucleotide sequences for Genomic DNA ###############################################
#########################################################################################################
>Adapter 1
GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG
>Adapter 2
ACACTCTTTCCCTACACGACGCTCTTCCGATCT
>PCR Primer 1
AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
>PCR Primer 2
CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT
>Genomic DNA Sequencing Primer
ACACTCTTTCCCTACACGACGCTCTTCCGATCT
##########################################################################################################
### 8. Illumina Paired End DNA oligonucleotide sequences #################################################
##########################################################################################################
>PE Adapter 1
GATCGGAAGAGCGGTTCAGCAGGAATGCCGAG
>PE Adapter 2
ACACTCTTTCCCTACACGACGCTCTTCCGATCT
>PE PCR Primer 1.0
AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
>PE PCR Primer 2.0
CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT
>PE Read 1 Sequencing Primer
ACACTCTTTCCCTACACGACGCTCTTCCGATCT
>PE Read 2 Sequencing Primer
CGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT
#########################################################################################################
### 9. Illumina Oligonucleotide sequences for the Multiplexing Sample Prep Oligo Only Kit ###############
#########################################################################################################
>Multiplexing Adapter 1
GATCGGAAGAGCACACGTCT
>Multiplexing Adapter 2
ACACTCTTTCCCTACACGACGCTCTTCCGATCT
>Multiplexing PCR Primer 1.0
AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
>Multiplexing PCR Primer 2.0
GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT
>Multiplexing Read 1 Sequencing Primer
ACACTCTTTCCCTACACGACGCTCTTCCGATCT
>Multiplexing Index Read Sequencing Primer
GATCGGAAGAGCACACGTCTGAACTCCAGTCAC
>Multiplexing Read 2 Sequencing Primer
GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT
>PCR Primer, Index 1
CAAGCAGAAGACGGCATACGAGATCGTGATGTGACTGGAGTTC
>PCR Primer, Index 2
CAAGCAGAAGACGGCATACGAGATACATCGGTGACTGGAGTTC
>PCR Primer, Index 3
CAAGCAGAAGACGGCATACGAGATGCCTAAGTGACTGGAGTTC
>PCR Primer, Index 4
CAAGCAGAAGACGGCATACGAGATTGGTCAGTGACTGGAGTTC
>PCR Primer, Index 5
CAAGCAGAAGACGGCATACGAGATCACTGTGTGACTGGAGTTC
>PCR Primer, Index 6
CAAGCAGAAGACGGCATACGAGATATTGGCGTGACTGGAGTTC
>PCR Primer, Index 7
CAAGCAGAAGACGGCATACGAGATGATCTGGTGACTGGAGTTC
>PCR Primer, Index 8
CAAGCAGAAGACGGCATACGAGATTCAAGTGTGACTGGAGTTC
>PCR Primer, Index 9
CAAGCAGAAGACGGCATACGAGATCTGATCGTGACTGGAGTTC
>PCR Primer, Index 10
CAAGCAGAAGACGGCATACGAGATAAGCTAGTGACTGGAGTTC
>PCR Primer, Index 11
CAAGCAGAAGACGGCATACGAGATGTAGCCGTGACTGGAGTTC
>PCR Primer, Index 12
CAAGCAGAAGACGGCATACGAGATTACAAGGTGACTGGAGTTC
##########################################################################################################
### 10. Illumina DpnII expression ###############################
### from http://www.omicsoft.com/downloads/ngs/contamination_list/v1.txt ###############################
##########################################################################################################
>Illumina DpnII expression Adapter 1
ACAGGTTCAGAGTTCTACAGTCCGAC
>Illumina DpnII expression Adapter 2
CAAGCAGAAGACGGCATACGA
>Illumina DpnII expression PCR Primer 1
CAAGCAGAAGACGGCATACGA
>Illumina DpnII expression PCR Primer 2
AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA
>Illumina DpnII expression Sequencing Primer
CGACAGGTTCAGAGTTCTACAGTCCGACGATC
#########################################################################################################
### 11. Illumina DpnII Gex ##############################
### from http://www.omicsoft.com/downloads/ngs/contamination_list/v1.txt ##############################
#########################################################################################################
>Illumina DpnII Gex Adapter 1
GATCGTCGGACTGTAGAACTCTGAAC
>Illumina DpnII Gex Adapter 1.01
ACAGGTTCAGAGTTCTACAGTCCGAC
>Illumina DpnII Gex Adapter 2
CAAGCAGAAGACGGCATACGA
>Illumina DpnII Gex Adapter 2.01
TCGTATGCCGTCTTCTGCTTG
>Illumina DpnII Gex PCR Primer 1
CAAGCAGAAGACGGCATACGA
>Illumina DpnII Gex PCR Primer 2
AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA
>Illumina DpnII Gex Sequencing Primer
CGACAGGTTCAGAGTTCTACAGTCCGACGATC
##########################################################################################################
### 12. Illumina NlaIII expression ###############################
### from http://www.omicsoft.com/downloads/ngs/contamination_list/v1.txt ###############################
##########################################################################################################
>Illumina NlaIII expression Adapter 1
ACAGGTTCAGAGTTCTACAGTCCGACATG
>Illumina NlaIII expression Adapter 2
CAAGCAGAAGACGGCATACGA
>Illumina NlaIII expression PCR Primer 1
CAAGCAGAAGACGGCATACGA
>Illumina NlaIII expression PCR Primer 2
AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA
>Illumina NlaIII expression Sequencing Primer
CCGACAGGTTCAGAGTTCTACAGTCCGACATG
#########################################################################################################
### 13. Illumina Small RNA Kits v1 and v1.5 ##############################
### from http://www.omicsoft.com/downloads/ngs/contamination_list/v1.txt ##############################
#########################################################################################################
>Illumina Small RNA Adapter 1
GTTCAGAGTTCTACAGTCCGACGATC
>Illumina Small RNA Adapter 2
TCGTATGCCGTCTTCTGCTTGT
>Illumina Small RNA RT Primer
CAAGCAGAAGACGGCATACGA
>Illumina Small RNA PCR Primer 1
CAAGCAGAAGACGGCATACGA
>Illumina Small RNA PCR Primer 2
AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA
>Illumina Small RNA Sequencing Primer
CGACAGGTTCAGAGTTCTACAGTCCGACGATC
########################################################################################################
### 14. SOLID 3 System Oligo ##############
### from http://www.omicsoft.com/downloads/ngs/contamination_list/v1.txt ##############
### SOLiD Fragment Library Barcoding Kit 1–96 protocol (Part Number 4448274 Rev. A) ##############
########################################################################################################
>ABI Dynabead EcoP Oligo
CTGATCTAGAGGTACCGGATCCCAGCAGT
>ABI Solid3 Adapter A
CTGCCCCGGGTTCCTCATTCTCTCAGCAGCATG
>ABI Solid3 Adapter B - Multiplex Library PCR-1
CCACTACGCCTCCGCTTTCCTCTCTATGGGCAGTCGGTGAT
>ABI Solid3 5' AMP Primer
CCACTACGCCTCCGCTTTCCTCTCTATG
>ABI Solid3 3' AMP Primer - Multiplex Library PCR-2
CTGCCCCGGGTTCCTCATTCT
>ABI Solid3 EF1 alpha Sense Primer
CATGTGTGTTGAGAGCTTC
>ABI Solid3 EF1 alpha Antisense Primer
GAAAACCAAAGTGGTCCAC
>ABI Solid3 GAPDH Forward Primer
TTAGCACCCCTGGCCAAGG
>ABI Solid3 GAPDH Reverse Primer
CTTACTCCTTGGAGGCCATG
>SOLID Multiplex Library P1 Adaptor
ATCACCGACTGCCCATAGAGAGGTT
########################################################################################################
### 15. Roche 454 Adaptors ######
### from http://nebc.nerc.ac.uk/bioinformatics/documentation/mira/html/mira_faq.html#section_5 ######
### http://sourceforge.net/apps/mediawiki/wgs-assembler/index.php?title=SffToCA ######
### ftp://ftp.ncbi.nih.gov/pub/UniVec/UniVec
########################################################################################################
>5' 454 adaptor
GCCTCCCTCGCGCCATCAGATCGTAGGCACCTGAAA
>3' 454 adaptor
GCCTTGCCAGCCCGCTCAGATTGATGGTGCCTACAG
>454 Adaptor A
CTGAGACAGGGAGGGAACAGATGGGACACGCAGGGATGAGATGG
>454 Adaptor B
CTGAGACACGCAACAGGGGATAGGCAAGGCACACAGGGGATAGG
>gnl|uv|NGB00599.1:1-47 Evrogen Mint 454 PCR Primer
ACGCAGAGTGGCCGAGGCGGCCTTTTGTCTTTTCTTCTGTTTCTTTT
>gnl|uv|NGB00385.1:1-44 454 FLX linker
GTTGGAACCGAAAGGGTTTGAATTCAAACCCTTTCGGTTCCAAC
>gnl|uv|NGB00386.1:1-42 454 Titanium linker
TCGTATAACTTCGTATAATGTATGCTATACGAAGTTATTACG
>gnl|uv|NGB00417.1:1-40 454 Life Sciences GS FLX Titanium MID-1 Adaptor A
CCATCTCATCCCTGCGTGTCTCCGACTCAGACGAGTGCGT
>Ti-MID1-Aprime
ACGCACTCGTCTGAGTCGGAGA
>gnl|uv|NGB00418.1:1-40 454 Life Sciences GS FLX Titanium MID-2 Adaptor A
CCATCTCATCCCTGCGTGTCTCCGACTCAGACGCTCGACA
>gnl|uv|NGB00419.1:1-40 454 Life Sciences GS FLX Titanium MID-3 Adaptor A
CCATCTCATCCCTGCGTGTCTCCGACTCAGAGACGCACTC
>gnl|uv|NGB00420.1:1-40 454 Life Sciences GS FLX Titanium MID-4 Adaptor A
CCATCTCATCCCTGCGTGTCTCCGACTCAGAGCACTGTAG
>gnl|uv|NGB00421.1:1-40 454 Life Sciences GS FLX Titanium MID-5 Adaptor A
CCATCTCATCCCTGCGTGTCTCCGACTCAGATCAGACACG
>gnl|uv|NGB00422.1:1-40 454 Life Sciences GS FLX Titanium MID-6 Adaptor A
CCATCTCATCCCTGCGTGTCTCCGACTCAGATATCGCGAG
>gnl|uv|NGB00423.1:1-40 454 Life Sciences GS FLX Titanium MID-7 Adaptor A
CCATCTCATCCCTGCGTGTCTCCGACTCAGCGTGTCTCTA
>gnl|uv|NGB00424.1:1-40 454 Life Sciences GS FLX Titanium MID-8 Adaptor A
CCATCTCATCCCTGCGTGTCTCCGACTCAGCTCGCGTGTC
>gnl|uv|NGB00425.1:1-40 454 Life Sciences GS FLX Titanium MID-10 Adaptor A
CCATCTCATCCCTGCGTGTCTCCGACTCAGTCTCTATGCG
>gnl|uv|NGB00426.1:1-40 454 Life Sciences GS FLX Titanium MID-11 Adaptor A
CCATCTCATCCCTGCGTGTCTCCGACTCAGTGATACGTCT
>gnl|uv|NGB00427.1:1-40 454 Life Sciences GS FLX Titanium MID-13 Adaptor A
CCATCTCATCCCTGCGTGTCTCCGACTCAGCATAGTAGTG
>gnl|uv|NGB00428.1:1-40 454 Life Sciences GS FLX Titanium MID-14 Adaptor A
CCATCTCATCCCTGCGTGTCTCCGACTCAGCGAGAGATAC
>gnl|uv|NGB00429.1:1-40 454 Life Sciences GS FLX Titanium MID-15 Adaptor A
CCATCTCATCCCTGCGTGTCTCCGACTCAGATACGACGTA
>gnl|uv|NGB00430.1:1-40 454 Life Sciences GS FLX Titanium MID-16 Adaptor A
CCATCTCATCCCTGCGTGTCTCCGACTCAGTCACGTACTA
>gnl|uv|NGB00431.1:1-40 454 Life Sciences GS FLX Titanium MID-17 Adaptor A
CCATCTCATCCCTGCGTGTCTCCGACTCAGCGTCTAGTAC
>gnl|uv|NGB00432.1:1-40 454 Life Sciences GS FLX Titanium MID-18 Adaptor A
CCATCTCATCCCTGCGTGTCTCCGACTCAGTCTACGTAGC
>gnl|uv|NGB00433.1:1-40 454 Life Sciences GS FLX Titanium MID-19 Adaptor A
CCATCTCATCCCTGCGTGTCTCCGACTCAGTGTACTACTC
>gnl|uv|NGB00434.1:1-40 454 Life Sciences GS FLX Titanium MID-20 Adaptor A
CCATCTCATCCCTGCGTGTCTCCGACTCAGACGACTACAG
>gnl|uv|NGB00435.1:1-40 454 Life Sciences GS FLX Titanium MID-21 Adaptor A
CCATCTCATCCCTGCGTGTCTCCGACTCAGCGTAGACTAG
>gnl|uv|NGB00436.1:1-40 454 Life Sciences GS FLX Titanium MID-22 Adaptor A
CCATCTCATCCCTGCGTGTCTCCGACTCAGTACGAGTATG
>gnl|uv|NGB00437.1:1-40 454 Life Sciences GS FLX Titanium MID-23 Adaptor A
CCATCTCATCCCTGCGTGTCTCCGACTCAGTACTCTCGTG
>gnl|uv|NGB00438.1:1-40 454 Life Sciences GS FLX Titanium MID-24 Adaptor A
CCATCTCATCCCTGCGTGTCTCCGACTCAGTAGAGACGAG
>gnl|uv|NGB00439.1:1-40 454 Life Sciences GS FLX Titanium MID-25 Adaptor A
CCATCTCATCCCTGCGTGTCTCCGACTCAGTCGTCGCTCG
>gnl|uv|NGB00440.1:1-40 454 Life Sciences GS FLX Titanium MID-26 Adaptor A
CCATCTCATCCCTGCGTGTCTCCGACTCAGACATACGCGT
>gnl|uv|NGB00441.1:1-40 454 Life Sciences GS FLX Titanium MID-27 Adaptor A
CCATCTCATCCCTGCGTGTCTCCGACTCAGACGCGAGTAT
>gnl|uv|NGB00442.1:1-40 454 Life Sciences GS FLX Titanium MID-28 Adaptor A
CCATCTCATCCCTGCGTGTCTCCGACTCAGACTACTATGT
>gnl|uv|NGB00443.1:1-40 454 Life Sciences GS FLX Titanium MID-29 Adaptor A
CCATCTCATCCCTGCGTGTCTCCGACTCAGACTGTACAGT
>gnl|uv|NGB00444.1:1-40 454 Life Sciences GS FLX Titanium MID-30 Adaptor A
CCATCTCATCCCTGCGTGTCTCCGACTCAGAGACTATACT
>gnl|uv|NGB00445.1:1-40 454 Life Sciences GS FLX Titanium MID-31 Adaptor A
CCATCTCATCCCTGCGTGTCTCCGACTCAGAGCGTCGTCT
>gnl|uv|NGB00446.1:1-40 454 Life Sciences GS FLX Titanium MID-32 Adaptor A
CCATCTCATCCCTGCGTGTCTCCGACTCAGAGTACGCTAT
>gnl|uv|NGB00447.1:1-40 454 Life Sciences GS FLX Titanium MID-33 Adaptor A
CCATCTCATCCCTGCGTGTCTCCGACTCAGATAGAGTACT
>gnl|uv|NGB00448.1:1-40 454 Life Sciences GS FLX Titanium MID-34 Adaptor A
CCATCTCATCCCTGCGTGTCTCCGACTCAGCACGCTACGT
>gnl|uv|NGB00449.1:1-40 454 Life Sciences GS FLX Titanium MID-35 Adaptor A
CCATCTCATCCCTGCGTGTCTCCGACTCAGCAGTAGACGT
>gnl|uv|NGB00450.1:1-40 454 Life Sciences GS FLX Titanium MID-36 Adaptor A
CCATCTCATCCCTGCGTGTCTCCGACTCAGCGACGTGACT
>gnl|uv|NGB00451.1:1-40 454 Life Sciences GS FLX Titanium MID-37 Adaptor A
CCATCTCATCCCTGCGTGTCTCCGACTCAGTACACACACT
>gnl|uv|NGB00452.1:1-40 454 Life Sciences GS FLX Titanium MID-38 Adaptor A
CCATCTCATCCCTGCGTGTCTCCGACTCAGTACACGTGAT
>gnl|uv|NGB00453.1:1-40 454 Life Sciences GS FLX Titanium MID-39 Adaptor A
