Anurag Daware's repositories
3C_tutorial
Simple codes and lines to process 3C/Hi-C data
agent
Lift same species genome co-ordinates from one assembly to another
Axiom-LiftOver-BLAST
Coordinate conversion of Axiom SNP array markers using BLAST
bioinfo-tools
Just a collection of (often poor) scripts to do various bits of bioinformatics stuff I find myself needing to do.
bioinformatics-workflows
minimal example implementations for bioinformatics workflow managers
bionano_tools
Helper scripts for working with Bionano data
BioNanoAnalyst
BioNanoAnalyst is a tool providing GUI to assess the genome assembly quality using BioNano data.
cue
Deep learning framework for SV calling and genotyping
diploidocus
Diploid genome assembly analysis tools
docker-builds
A collection of useful Docker builds
Explore-phenotype
The script takes multi-year, multi-replication enviorment data as input and does exploratory analyisis (histogram, box plot), calculates baisc statistcs (mean, SD, missingness) and perform imputation (save imputed phenotype)
GenoToolBox
A box of genomics tools
hic-data-analysis-bootcamp
Workshop on measuring, analyzing, and visualizing the 3D genome with Hi-C data.
Maize_NC358
The repository for codes developed to generated the Maize NC358 assemblies and analyses.
markdown-editor
Live (Github-flavored) Markdown Editor
nf-anvio-pangenome
Analyze a set of genomes with the anvi'o pangenome pipeline
Omni-C
Omni-C data processing documentation and scripts
OpenBioinformaticsWorkshops
Open courseware for workshops in applied bioinformatics
plant.annot
Annotation pipeline for plant genomes by PGSB
population_genomics
Scripts
protocols
Our laboratory repository
pyOverChain
a python pipeline to generate chain files between different genome assemblies for LiftOver.
teloclip
A tool for the recovery of unassembled telomeres from soft-clipped read alignments.
unix_oneliners
Scripts and one-liners to do data formatting and simple tasks required by fellow biologists.
variant-calling-bwa-gatk4
Reads to variants workflow involving fastp-BWA-GATK
vgp-assembly
VGP repository for the genome assembly working group