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graph improvement
Gael MILLOT authored
a7f67a07
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bin
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Licence.txt
README.md
main.nf
nextflow.config
README.md
Usage Requirement
Nextflow Dependencies: Nextflow Version
License: GPL-3.0 Dependencies: Apptainer Version
Dependencies: Graphviz Version



TABLE OF CONTENTS



AIM

  • Annotation of mRNA sequencing of the Immunoglobuline Heavy or Light variable region (fasta file sequences).
  • Clustering of the annotated sequences into clonal groups (same germline origin).
  • Tree visualization of the clonal groups.



WARNINGS

  • Right now, only dedicated to the analysis of VDJ repertoires (corresponding to the germlines/imgt/<SPECIES>/vdj folder of the IMGT database.
  • To make the repertoires contingency tables and heatmaps, the script currently takes the first annotation of the imgt annotation if several are presents in the v_call or j_call column of the all_passed_seq.tsv file.



CONTENT

Files and folder Description
main.nf File that can be executed using a linux terminal, a MacOS terminal or Windows 10 WSL2.
nextflow.config Parameter settings for the main.nf file. Users have to open this file, set the desired settings and save these modifications before execution.
bin folder Contains files required by the main.nf file.
xlsx2fasta.R Accessory file that creates all the fasta files required from a .xlsx file. To use it, 1) open the file, 2) complete the "Parameters that need to be set by the user" section, 3) save the modifications and 4) run the file in R.
Licence.txt Licence of the release.



INPUT

Required files
A folder (zipped or not) containing nucleotide fasta files, each containing a single sequence. Use xlsx2fasta.R (https://github.com/gael-millot/xlsx2fasta) if sequences are in a .xlsx file.
A metadata file (optional) for adding informations in the results.

The dataset used in the nextflow.config file, as example, is available at https://zenodo.org/records/8403994.


Use this code to split a multi sequence fasta file into fasta files made of a single sequence:

FASTA_FILE="./test.fasta" # add path and name of the fasta file here
awk -v slice_size=1 -v prefix="cut" '$1 ~ /^>/{nbSeq++; currSlice=int((nbSeq-1)/slice_size)+1; myOutFile=prefix"_"currSlice".fasta"}{print $0 > myOutFile}' ${FASTA_FILE}



HOW TO RUN

1. Prerequisite

Installation of:
nextflow DSL2
Graphviz, sudo apt install graphviz for Linux ubuntu
Apptainer



2. Local running (personal computer)

2.1. main.nf file in the personal computer

  • Mount a server if required:
DRIVE="Z" # change the letter to fit the correct drive
sudo mkdir /mnt/share
sudo mount -t drvfs $DRIVE: /mnt/share

Warning: if no mounting, it is possible that nextflow does nothing, or displays a message like:

Launching `main.nf` [loving_morse] - revision: d5aabe528b
/mnt/share/Users
  • Run the following command from where the main.nf and nextflow.config files are (example: \wsl$\Ubuntu-20.04\home\gael):
nextflow run main.nf -c nextflow.config

with -c to specify the name of the config file used.



2.3. main.nf file in the public gitlab repository

Run the following command from where you want the results:

nextflow run -hub pasteur gmillot/repertoire_profiler -r v1.0.0



3. Distant running (example with the Pasteur cluster)

3.1. Pre-execution

Copy-paste this after having modified the EXEC_PATH variable:

EXEC_PATH="/pasteur/helix/projects/BioIT/gmillot/repertoire_profiler" # where the bin folder of the main.nf script is located
export CONF_BEFORE=/opt/gensoft/exe # on maestro

export JAVA_CONF=java/13.0.2
export JAVA_CONF_AFTER=bin/java # on maestro
export APP_CONF=apptainer/1.3.5
export APP_CONF_AFTER=bin/apptainer # on maestro
export GIT_CONF=git/2.39.1
export GIT_CONF_AFTER=bin/git # on maestro
export GRAPHVIZ_CONF=graphviz/2.42.3
export GRAPHVIZ_CONF_AFTER=bin/graphviz # on maestro

MODULES="${CONF_BEFORE}/${JAVA_CONF}/${JAVA_CONF_AFTER},${CONF_BEFORE}/${APP_CONF}/${APP_CONF_AFTER},${CONF_BEFORE}/${GIT_CONF}/${GIT_CONF_AFTER}/${GRAPHVIZ_CONF}/${GRAPHVIZ_CONF_AFTER}"
cd ${EXEC_PATH}
chmod 755 ${EXEC_PATH}/bin/*.* # not required if no bin folder
module load ${JAVA_CONF} ${APP_CONF} ${GIT_CONF} ${GRAPHVIZ_CONF}



3.2. main.nf file in a cluster folder

Modify the second line of the code below, and run from where the main.nf and nextflow.config files are (which has been set thanks to the EXEC_PATH variable above):

HOME_INI=$HOME
HOME="${HELIXHOME}/repertoire_profiler/" # $HOME changed to allow the creation of .nextflow into /$HELIXHOME/repertoire_profiler/, for instance. See NFX_HOME in the nextflow software script
nextflow run --modules ${MODULES} main.nf -c nextflow.config
HOME=$HOME_INI



3.3. main.nf file in the public gitlab repository

Modify the first and third lines of the code below, and run (results will be where the EXEC_PATH variable has been set above):

VERSION="v1.0"
HOME_INI=$HOME
HOME="${HELIXHOME}/repertoire_profiler/" # $HOME changed to allow the creation of .nextflow into /$HELIXHOME/repertoire_profiler/, for instance. See NFX_HOME in the nextflow software script
nextflow run --modules ${MODULES} -hub pasteur gmillot/repertoire_profiler -r $VERSION -c $HOME/nextflow.config
HOME=$HOME_INI



4. Error messages and solutions

Message 1

Unknown error accessing project `gmillot/repertoire_profiler` -- Repository may be corrupted: /pasteur/sonic/homes/gmillot/.nextflow/assets/gmillot/repertoire_profiler

Purge using:

rm -rf /pasteur/sonic/homes/gmillot/.nextflow/assets/gmillot*

Message 2

WARN: Cannot read project manifest -- Cause: Remote resource not found: https://gitlab.pasteur.fr/api/v4/projects/gmillot%2Frepertoire_profiler

Contact Gael Millot (distant repository is not public).

Message 3

permission denied

Use chmod to change the user rights. Example linked to files in the bin folder:

chmod 755 bin/*.*



OUTPUT

An example of results obtained with the dataset is present at this address: https://zenodo.org/record/8403994/files/repertoire_profiler.zip

Complete informations are in the Protocol 144-rev0 Ig clustering - Immcantation.docx (contact Gael Millot).

Mandatory elements:

repertoire_profiler_<UNIQUE_ID> folder Description
reports Folder containing all the reports of the different processes, including the nextflow.config file used.
repertoires Folder containing the repertoires, i.e., contingency tables of the VDJ allele usage from the all_passed_seq.tsv file (see below). Warning: the script currently takes the first annotation of the imgt annotation if several are presents in the v_call or j_call column of the all_passed_seq.tsv file. (e.g., v_call with IGKV1-39*01,IGKV1D-39*01), so that contingencies are identical to those from the donut frequencies, that use germline_v_call and germline_j_call columns (allele reassignment by the CreateGermlines.py tool of immcantation)
png Folder containing the graphs in png format.
svg Folder containing the graphs in svg vectorial format.
RData Folder containing, for each clonal group, objects that can be used in R to further analyze of plot the data:
  • db: tibble data frame resulting from the import by the alakazam::readChangeoDb() function
  • clones: db in the airClone format
  • trees: output of the dowser::getTrees() function using the clones object as input (igphylm tree)


    • Also contains the all_trees.RData file that combine the trees R objects of the different files in a single trees object.
seq_distance.pdf Distribution of the distances between the two nearest sequences (see the nearest_distance column in the all_passed_seq.tsv file).
donuts.pdf donut plots showing the frequency of sequences per clonal groups, among:
  • all: all the passed sequences (all_passed_seq.tsv output file).
  • annotated: as the "all" donut but using all the passed sequences that have been annotated using the meta_name_replacement parameter of the nextflow.config file if not "NULL".
  • trees: all the sequences used for germline trees (germ_tree_seq.tsv output file).
repertoire.pdf heatmap of the files from the repertoires folder (see above), showing the frequency of alleles used among all the all passed sequences ("all"), non empty cells ("non-zero") and "annotated" sequences (if metadata are provided). Non-zero means that unused alleles are removed from the heatmap (empty row or column). Warning: to build the repertoire contingencies, the script currently takes the first annotation of the imgt annotation if several are presents in the v_call or j_call column of the all_passed_seq.tsv file (see the all_passed_seq_several_annot_igmt.tsv file below)
germ_tree.pdf Phylogenic trees of the sequences that belong to a clonal (supposedly germline) group made of at least n sequences, n being set by the nb_seq_per_clone parameter in the nextflow.config file (one page per clonal group). Warning: clonal group full names are those given by dowser::formatClones, i.e., those from germinal_v_call and germinal_j_call from the all_passed_seq.tsv file.
germ_no_tree.pdf All the clonal groups with less than n sequences, n being set by the nb_seq_per_clone parameter in the nextflow.config file (one page per clonal group). Clonal group nformation is recapitulated in each page.
donut_stat.tsv stats associated to the donuts.pdf file.
igblast_unaligned_seq.tsv Names of sequences that failed to be annotated by igblast (empty file if all the sequences are annotated).
igblast_aligned_seq.tsv Names of sequences annotated by igblast (more precisely by MakeDb.py igblast). If empty, generate a subsequent nextflow failure. The number lines in igblast_unaligned_seq.tsv and igblast_aligned_seq.tsv is equal to the number of submitted .fasta files.
productive_seq.tsv Sequences annotated by igblast (see the unproductive_seq.tsv file for sequences that failed to be productive annotated by igblast). Productive means: (1) coding region has an open reading frame, (2) no defect in the start codon, splicing sites or regulatory elements, (3) no internal stop codons, (4) an in-frame junction region.
all_passed_seq.tsv Sequences from the productive_seq.tsv file with germline clustering (clone ID), allele reannotation (germinal_v_call and germinal_j_call columns), mutation load, distance and sequence nickname (annotation from the metadata file) added. Warning: the number of sequences (i.e., rows) can be lower than in the productive_seq.tsv file due to sequences that failed to be clone assigned (see the non_clone_assigned_sequence.tsv file).
Column description:
  • sequence_id: Unique query sequence identifier for the Rearrangement. Most often this will be the input sequence header or a substring thereof, but may also be a custom identifier defined by the tool in cases where query sequences have been combined in some fashion prior to alignment. When downloaded from an AIRR Data Commons repository, this will usually be a universally unique record locator for linking with other objects in the AIRR Data Model.
  • sequence: The query nucleotide sequence. Usually, this is the unmodified input sequence, which may be reverse complemented if necessary. In some cases, this field may contain consensus sequences or other types of collapsed input sequences if these steps are performed prior to alignment.
  • rev_comp: True if the alignment is on the opposite strand (reverse complemented) with respect to the query sequence. If True then all output data, such as alignment coordinates and sequences, are based on the reverse complement of 'sequence'.
  • productive: True if the V(D)J sequence is predicted to be productive.
  • v_call: V gene with allele. If referring to a known reference sequence in a database the relevant gene/allele nomenclature should be followed (e.g., IGHV4-59*01 if using IMGT/GENE-DB).
  • d_call: First or only D gene with allele. If referring to a known reference sequence in a database the relevant gene/allele nomenclature should be followed (e.g., IGHD3-10*01 if using IMGT/GENE-DB).
  • j_call: J gene with allele. If referring to a known reference sequence in a database the relevant gene/allele nomenclature should be followed (e.g., IGHJ4*02 if using IMGT/GENE-DB).
  • sequence_alignment: Aligned portion of query sequence, including any indel corrections or numbering spacers, such as IMGT-gaps. Typically, this will include only the V(D)J region, but that is not a requirement.
  • germline_alignment: Assembled, aligned, full-length inferred germline sequence spanning the same region as the sequence_alignment field (typically the V(D)J region) and including the same set of corrections and spacers (if any). Thus, If well understood, this sequence is built from VDJ sequences in databases that match the sequence in sequence_alignment, with gap included only. Nucleotides can be different with sequence_alignment. Warning: sequences with the same clone_ID can have different germline_aligments.
  • junction: Junction region nucleotide sequence, where the junction is defined as the CDR3 plus the two flanking conserved codons.
  • junction_aa: Amino acid translation of the junction.
  • v_cigar: CIGAR string for the V gene alignment. See protocol 50
  • d_cigar: CIGAR string for the first or only D gene alignment. See protocol 50
  • j_cigar: CIGAR string for the J gene alignment. See protocol 50
  • stop_codon: True if the aligned sequence contains a stop codon.
  • vj_in_frame: True if the V and J gene alignments are in-frame.
  • locus: Gene locus (chain type). Note that this field uses a controlled vocabulary that is meant to provide a generic classification of the locus, not necessarily the correct designation according to a specific nomenclature.
  • junction_length: Number of nucleotides in the junction sequence.
  • np1_length: Number of nucleotides between the V gene and first D gene alignments or between the V gene and J gene alignments.
  • np2_length: Number of nucleotides between either the first D gene and J gene alignments or the first D gene and second D gene alignments.
  • v_sequence_start: Start position of the V gene in the query sequence (1-based closed interval).
  • v_sequence_end: End position of the V gene in the query sequence (1-based closed interval).
  • v_germline_start: Alignment start position in the V gene reference sequence (1-based closed interval).
  • v_germline_end: Alignment end position in the V gene reference sequence (1-based closed interval).
  • d_sequence_start: Start position of the first or only D gene in the query sequence. (1-based closed interval).
  • d_sequence_end: End position of the first or only D gene in the query sequence. (1-based closed interval).
  • d_germline_start: Alignment start position in the D gene reference sequence for the first or only D gene (1-based closed interval).
  • d_germline_end: Alignment end position in the D gene reference sequence for the first or only D gene (1-based closed interval).
  • j_sequence_start: Start position of the J gene in the query sequence (1-based closed interval).
  • j_sequence_end: End position of the J gene in the query sequence (1-based closed interval).
  • j_germline_start: Alignment start position in the J gene reference sequence (1-based closed interval).
  • j_germline_end: Alignment end position in the J gene reference sequence (1-based closed interval).
  • v_score: Alignment score for the V gene. See raw score
  • v_identity: Fractional identity for the V gene alignment (proportion)
  • v_support: V gene alignment E-value, p-value, likelihood, probability or other similar measure of support for the V gene assignment as defined by the alignment tool.
  • d_score: Alignment score for the first or only D gene alignment.
  • d_identity: Fractional identity for the first or only D gene alignment.
  • d_support: D gene alignment E-value, p-value, likelihood, probability or other similar measure of support for the first or only D gene as defined by the alignment tool.
  • j_score: Alignment score for the J gene alignment.
  • j_identity: Fractional identity for the J gene alignment.
  • j_support: J gene alignment E-value, p-value, likelihood, probability or other similar measure of support for the J gene assignment as defined by the alignment tool.
  • fwr1: Nucleotide sequence of the aligned FWR1 region of the query sequence (i.e., sequence_alignment field).
  • fwr2: Nucleotide sequence of the aligned FWR2 region of the query sequence (i.e., sequence_alignment field).
  • fwr3: Nucleotide sequence of the aligned FWR3 region of the query sequence (i.e., sequence_alignment field).
  • fwr4: Nucleotide sequence of the aligned FWR4 region of the query sequence (i.e., sequence_alignment field).
  • cdr1: Nucleotide sequence of the aligned CDR1 region of the query sequence (i.e., sequence_alignment field).
  • cdr2: Nucleotide sequence of the aligned CDR2 region of the query sequence (i.e., sequence_alignment field).
  • cdr3: Nucleotide sequence of the aligned CDR3 region of the query sequence (i.e., sequence_alignment field).
  • sequence_alignment_aa: Translation in aa of the sequence_alignment column
  • clone_id: Clone number. A same clone_id gathers all the sequences that putatively come from a same germline cell.
  • germline_alignment_d_mask: as germline_alignment but with D masked (i.e., replaced by N, in the middle of the CDR3). Because the D-segment call for B cell receptor alignments is often low confidence, the default germline format (-g dmask) places Ns in the N/P and D-segments of the junction region rather than using the D-segment assigned during reference alignment; this can be modified to generate a complete germline (-g full) or a V-segment only germline (-g vonly)
  • germline_v_call: V germline cassette
  • germline_d_call: D germline cassette (usually NA)
  • germline_j_call: J germline cassette
  • mu_count_cdr_r: number of replacement mutations in CDR1 and CDR2 of the V-segment (comparing column sequence_alignment and column germline_alignment_d_mask, see https://shazam.readthedocs.io/en/stable/topics/observedMutations/#value).
  • mu_count_cdr_s: number of silent mutations in CDR1 and CDR2 of the V-segment.
  • mu_count_fwr_r: number of replacement mutations in FWR1, FWR2 and FWR3 of the V-segment.
  • mu_count_fwr_s: number of silent mutations in FWR1, FWR2 and FWR3 of the V-segment.
  • mu_count: number of replacement and silent mutations (sum of the previous columns)
  • mu_freq_cdr_r: frequency of replacement mutations in CDR1 and CDR2 of the V-segment (if frequency=TRUE, R and S mutation frequencies are calculated over the number of non-N positions in the specified regions).
  • mu_freq_cdr_s: frequency of silent mutations in CDR1 and CDR2 of the V-segment (idem).
  • mu_freq_fwr_r: frequency of replacement mutations in FWR1, FWR2 and FWR3 of the V-segment (idem).
  • mu_freq_fwr_s: frequency of silent mutations in FWR1, FWR2 and FWR3 of the V-segment (idem).
  • mu_freq: frequency of replacement and silent mutations (sum of the previous columns)
  • dist_nearest: minimal distance from the nearest sequence using the model from the clone_model parameter (Haming by default). NA if no other sequences have same V, J and junction length or if another sequence is strictly identical (should be 0 but NA is returned)
all_passed_seq_several_annot_igmt.tsv Sequences from the all_passed_seq.tsv file with several annotation in the v_call and j_call columns, because several alleles had the best alignment using imgt blast (same )
unproductive_seq.tsv Sequences that failed productive annotations by igblast (empty file if all the sequences are productively annotated).
non_clone_assigned_sequence.tsv Productive sequences that failed to be assigned to a clone ID by the DefineClones.py function (empty file if all the sequences are assigned).
germ_tree_clone_id.tsv Clonal group IDs used in the germline tree analysis (clonal group with at least n sequences, n being set by the nb_seq_per_clone parameter in the nextflow.config file).
germ_tree_dismissed_clone_id.tsv Clonal group IDs not used in the germline tree analysis (clonal group with less than n sequences, n being set by the nb_seq_per_clone parameter in the nextflow.config file).
germ_tree_seq.tsv Sequences of the all_passed_seq.tsv file used in the germline tree analysis (clonal group with at least n sequences, n being set by the nb_seq_per_clone parameter in the nextflow.config file).
germ_tree_dismissed_seq.tsv Sequences of the all_passed_seq.tsv file not used in the germline tree analysis (clonal group with less than n sequences, n being set by the nb_seq_per_clone parameter in the nextflow.config file).
germ_tree_dup_seq_not_displayed.tsv Sequences file used in the germline tree analysis but not displayed in the graph, (1) because strictly identical to another sequence already in the tree and (2) because the tree_duplicate_seq parameter of the nextflow.config file has been set to "FALSE".



Optional elements only returned if the igblast_aa parameter is 'false' and if the input fasta are nucleotide sequences:

repertoire_profiler_xxxxx folder Description
aa Folder containing the translation of the alignment_sequence column of the productive_seq.tsv file in fasta files.
aligned_seq Folder containing the alignment_sequence column of the productive_seq.tsv file in fasta files.
aa.tsv File containing all the translation of the alignment_sequence column of the productive_seq.tsv file.



VERSIONS

The different releases are tagged here.



LICENCE

This package of scripts can be redistributed and/or modified under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. Distributed in the hope that it will be useful, but without any warranty; without even the implied warranty of merchandability or fitness for a particular purpose. See the GNU General Public License for more details at https://www.gnu.org/licenses or in the Licence.txt attached file.



CITATION

Version V10.3:

Dejoux A, Zhu Q, Ganneau C, Goff OR, Godon O, Lemaitre J, Relouzat F, Huetz F, Sokal A, Vandenberghe A, Pecalvel C, Hunault L, Derenne T, Gillis CM, Iannascoli B, Wang Y, Rose T, Mertens C, Nicaise-Roland P; NASA Study Group; England P, Mahévas M, de Chaisemartin L, Le Grand R, Letscher H, Saul F, Pissis C, Haouz A, Reber LL, Chappert P, Jönsson F, Ebo DG, Millot GA, Bay S, Chollet-Martin S, Gouel-Chéron A, Bruhns P. Rocuronium-specific antibodies drive perioperative anaphylaxis but can also function as reversal agents in preclinical models. Sci Transl Med. 2024 Sep 11;16(764):eado4463. doi: 10.1126/scitranslmed.ado4463. Epub 2024 Sep 11. PMID: 39259810.



CREDITS

Pascal Chappert, INSERM U1151 Institut Necker Enfants Malades, Paris, France

Frédéric Lemoine, Bioinformatics and Biostatistics Hub, Institut Pasteur, Paris, France

Gael A. Millot, Bioinformatics and Biostatistics Hub, Institut Pasteur, Paris, France



ACKNOWLEDGEMENTS

The developers & maintainers of the mentioned softwares and packages, including:

Special acknowledgement to Kenneth Hoehn, Yale School of Medicine, New Haven, CT, USA



WHAT'S NEW IN

v11.1

  • Option comment_char = '' of read.table() for all .R files with read.table() in bin

v11.0

  • Tree plots improved

v10.4

  • Donut plot legend corrected

v10.3

  • Spaces removed in file names
  • Spaces removed in the first line of each fasta file
  • .fas fasta extension allowed

v10.2

xlsx2fasta.R file: error fixed for the fasta by categ

v10.1

xlsx2fasta.R file improved to take into account the problem of NA

v10.0

xlsx2fasta.R file strongly improved to deal with empty sequences

v9.9

Bug fixed in xlsx2fasta.R

v9.8

Error fixed in the nextflow.config file about cute path

v9.7

Cute folder updated to 12.8 to fix the palette bug in fun_gg_donut()

v9.6

Bug in the metadata_check process fixed

v9.5

README improved so that now dataset and results are in zenodo

v9.4

bug fixed

v9.3

important check added for the metadata file

v9.2

  • repertoires now ok with a mix of IGK and IGL sequences
  • first annotation taken if several v or j allele annotation by imgt for the repertoires

v9.1

bug corrected for the meta_name_replacement parameter

v9.0

repertoire_profiler.nf and .config name changed so that now can be run from gitlab

v8.14

README file improved, that clarify the differences between sequence_alignment and germline_* sequences

v8.13

README file improved, that clarify if results are from the productive seq or all passed seq

v8.12

Check added for the metadata file of the meta_path parameter. But check the content of the first column of this file remains to be added

v8.11

bugs fixed

v8.10

bugs fixed

v8.9

ig_clustering name replaced everywhere by repertoire_profiler

v8.8

Quotes removed from all output files

v8.7

xlsx2fasta.R file modified so that it now split data according to each class of the categ parameter

v8.6

Minor aesthetic modifications in trees and donut

v8.5

Bugs fixed in distToNearest

v8.4

  • Bugs fixed in clone_assignment and get_tree with a new output file created non_clone_assigned_sequence.tsv
  • Bugs fixed in tree_vizu when no metadata

v8.3

  • Bug fixed in tree_vizu: now nb of removed seq are displayed again
  • Now annotated seq are colored

v8.2

Bug fixed in tree_vizu: now meta are displayed again

v8.1

Bug fixed in get_tree

v8.0

  • xlsx2fasta.R file modified so that fasta files have correct names
  • now trees.pdf return an empty graph (but with infos) for clonal groups without trees

v7.1

Clean version of the xlsx2fasta.R script: can now be run on any excel file

v7.0

  • Bug of the tree_seq_not_displayed.tsv file fixed
  • Number of seq removed added in tree leafs

v6.11

Code debbuged. tree_seq_not_displayed.tsv remains to be debugged

v6.10

Repertoires improved

v6.9

Repertoires added

v6.8

  • igblast_aa parameter not operational yet. igblast_aa = "true" does not work for the moment because no j data in the imgt database and no junction data are returned which block the clone_assignment process
  • tree_vizu process not sensitive to cache

v6.7

Problem of cache fixed for distance_hist process and bug fixed for empty pdf plot in this process. It was the name seq_distance, creating a replacement of the seq_distance.pdf file

v6.6

Names of metadata now systematically present in trees, even when identical sequences are removed, and bug fixed for empty pdf plot

v6.5

Code secured and bug fixed for NULL metadata file path

v6.4

Distances added in the returned productive_seq.tsv, now 3 histograms to help to set the distance threshold, many bugs fixed

v6.3

AA sequences added. Translation of the alignment_sequence column is added in the returned productive_seq.tsv and new aa.tsv file

v6.2

Supp donut added regarding clonal groups with functional annotation

v6.1

New parameters for the donut

v6.0

Distance histogram added Empty graphs added New parameters for the donut

v5.1

Metadata info added in donut plot

v5.0

Bug solved when the tree_meta_path_names parameter is a categorical column New tree_meta_name_replacement parameter

v4.4

Bug solved in seq_not_displayed.tsv file

v4.3

igblast_aa parameter removed from the .config file bug solved in tree_vizu

v4.2

Donut charts grouped in a single pdf

v4.1

seq_not_displayed.tsv file added to better understand the absence of seq in trees
V and J alleles added in the donut legend

v4.0

tree_meta_path modified so that it can now be a 'NULL' path
V and J alleles added in tree titles
Duplicated sequences can be removed or not from trees

v3.5

Bug solved

v3.4

Two Donut charts added

v3.3

Empty channel solved
Donut chart added

v3.2

README file updated for localization of the igblast database

v3.1

README file updated

v3.0

First version that provides trees of clonal groups

v2.1

xlsx2fasta.R file added | Nicer tree representation added

v2.0

Conversion into DSL2 ok

v1.0

First DSL1 version that works