TADbit

BWA-MEM2 — accelerated Burrows-Wheeler Aligner for mapping short DNA reads to reference genomes. Use when aligning Illumina WGS, WES, targeted panel, ChIP-seq, or ATAC-seq FASTQ reads. Drop-in replace

1 shared topic • 2 shared operations

HiC-Pro is an all-in-one pipeline for processing Hi-C sequencing data from raw FASTQ files to normalized contact matrices. Performs read alignment with Bowtie2, restriction-fragment assignment, valid-

1 shared topic • 2 shared operations

LSHTM PathogenSeq bioinformatics pipelines for pathogen whole-genome sequencing analysis, including TB-Profiler for Mycobacterium tuberculosis lineage and drug-resistance prediction from WGS data, Mal

1 shared topic • 2 shared operations

Use when performing precision HLA class I typing from NGS data with OptiType. Covers read mapping to HLA reference with YARA, Integer Linear Programming allele calling at 4-digit resolution for HLA-A,

1 shared topic • 2 shared operations

Use when working with vg — the variation graph toolkit — for pangenome graph construction, read mapping to variation graphs, and graph-aware variant calling. Builds genome graphs from VCF + reference

1 shared topic • 2 shared operations