This repository has been archived by the owner on Dec 7, 2021. It is now read-only.

Commits

Commits on Nov 7, 2019

update readme with publication link
cmdoret
committedNov 7, 2019

Commits on Aug 11, 2019

enable multithreading in trimmomatic calls and improve figure size for association mapping results
cmdoret
committedAug 11, 2019
add circos and blast to conda environment and update installation instructions
cmdoret
committedAug 11, 2019
simplify conda environment yaml and add third parties
cmdoret
committedAug 11, 2019

Commits on Aug 2, 2019

make bash code safer by quoting expansions and enforcing locales. Add utility script for coverage per sample.
cmdoret
committedAug 2, 2019

Commits on Jul 30, 2019

add adhoc analyses of distance to centromeres, fix indexing syntax in process_genomic and update conda env to be less stringent on versions
cmdoret
committedJul 30, 2019

Commits on Apr 17, 2019

Update data availability in readme
Cyril Matthey-Doret
committedApr 17, 2019

Commits on Apr 14, 2019

add zenodo DOI badge to README
Cyril Matthey-Doret
committedApr 14, 2019

Commits on Mar 25, 2019

add annotation analysis in csd regions
Cyril Matthey-Doret
committedMar 25, 2019
add annotation retrieval script
Cyril Matthey-Doret
committedMar 25, 2019

Commits on Nov 15, 2018

update readme with instructions to download data
cmdoret
committedNov 15, 2018

Commits on Oct 6, 2018

removed temporary files
cmdoret
committedOct 6, 2018
adjusted window size for centromere estimation.
cmdoret
committedOct 6, 2018
process_genomic.py now take into account the different genotypes of homozygous offspring to infer mother genotypes.
cmdoret
committedOct 6, 2018
process_genomic.py now take into account the different genotypes of homozygous offspring to infer mother genotypes.
cmdoret
committedOct 6, 2018

Commits on Aug 7, 2018

Commits on Aug 6, 2018

allow missssing contigs in correspondance file when running convert_GFF_coord.sh
cmdoret
committedAug 6, 2018
more time efficient computation of contig-correspondance between assemblies
cmdoret
committedAug 6, 2018
handle log file path in convertt_GFF_coord.sh and MCScanX_prep.sh
cmdoret
committedAug 6, 2018

Commits on Aug 5, 2018

fix makefile variable name for reference genome and remove debug logs from apply_bp2cm
cmdoret
committedAug 5, 2018

Commits on Aug 4, 2018

correct getopts syntax for log file option in corresp_contigs.sh
cmdoret
committedAug 4, 2018
correct argument name for log file of corresp_contigs.sh in Makefile and add log option in the script help
cmdoret
committedAug 4, 2018
fix line continuation in Makefile rule for collinearity
cmdoret
committedAug 4, 2018
include BAM indexing step in RNAseq processing script. Add cufflinks to cluster dependencies
cmdoret
committedAug 4, 2018

Commits on Aug 2, 2018

get argument parsing working with argparse in compute_PI.R
Cyril Matthey-Doret
committedAug 2, 2018

Commits on Jul 30, 2018

Use argparse instead of optparse for CL handling in R. Update Makefile, README, anaconda environment and comput_PI.R accordingly.
cmdoret
committedJul 30, 2018

Commits on Jul 29, 2018

Commits on Jul 28, 2018

fix default path of wgs reads and specify anaconda version in readme.
cmdoret
committedJul 28, 2018

Commits on Jul 27, 2018

fix markdown formatting in readme
cmdoret
committedJul 27, 2018
reformat markdown lists in readme.
cmdoret
committedJul 27, 2018
remove ggrepel from dependencies.
cmdoret
committedJul 27, 2018