Usman Rashid

From https://github.com/bowang-lab/BioReason-Pro

https://github.com/zengxiaofei/HapHiC

Python 3.14.3 & packages

https://github.com/wurmlab/sequenceserver

From https://github.com/marbl/Winnowmap

JuiceFlow container built on top of the latest nextflow container

Ubuntu with miniconda installed in /usr/local/miniconda3

https://github.com/phasegenomics/hic_qc

https://github.com/lbcb-sci/herro

https://github.com/NBISweden/AGAT.git

python:3.11.3-bullseye with select packages.

Tools needed for EDTA pipeline

GFFREAD and NCBI-BLAST+

Python Flask with select packages

Structural variant caller for low-depth long-read sequencing data

VarIant SimulatOR for short, long and linked reads

winnowmap=2.03, samtools=1.18, meryl=1.4.1

randomregion.r script packaged with VISOR

https://github.com/phasegenomics/juicebox_scripts

C code to validate a fasta file

https://github.com/aidenlab/3d-dna