Rimjhim Roy Choudhury's repositories
ComparativeGenomics
A pipeline for processing data in a comparative genomics project.
dna-seq-gatk-variant-calling
This Snakemake pipeline implements the GATK best-practices workflow
GWA_tutorial
A comprehensive tutorial about GWAS and PRS
ITIPs
Identification of transposable element insertion polymorphisms (TIPs) based on a pan-genome and large-scale resequencing data
jekyll-theme-minimal-resume
Simple Jekyll theme for a minimal resume website: https://jekyll-theme-minimal-resume.netlify.com/
Transposon80-80-80
Annotate transposable elements using the 80-80-80 rule (Wicker et al. 2007)
katacoda-scenarios-1
Katacoda Scenarios
plastid_sequence_analysis
Analysis of plastid sequence
popgen
Population genetics analyses
popgen-notes
Population genetics notes
r-conda
R and RStudio via conda packages in repo2docker
residual-tetrasomy
For characterization of residually tetrasomic regions
snakeDeepvariant
snakemake Deepvariant
So2
So2 TE Bioinformatic ressources -- Parisot et al. 2020
stacks_workflow
RADseq workflow built around STACKS
TE_ManAnnot
Accompanying repository for our publications on manual curation methods for Transposable Elements.
TEscripts
Scripts used in Transposable element annotation
wgd
Python package and CLI for whole-genome duplication related analyses