Sambamba mkdup

Use when working with MIP (Medical Information Process) — a workflow management system for clinical whole-genome and whole-exome sequencing analysis. Runs end-to-end rare disease (rd_dna, rd_rna) and

1 shared topic • 3 shared operations

Java command-line tools from the Broad Institute for manipulating high-throughput sequencing data and formats including BAM, CRAM, and VCF.

1 shared topic • 3 shared operations

Bracken (Bayesian Reestimation of Abundance with KrakEN) — statistical method for computing species-level abundance estimates from Kraken/Kraken2/KrakenUniq taxonomic classifications. Redistributes re

1 shared topic • 2 shared operations

IGV (Integrative Genomics Viewer) — high-performance Java desktop application for interactive visualization and exploration of genomic data. Supports BAM/CRAM alignments, VCF variants, BED/GFF annotat

1 shared topic • 2 shared operations

MACS2 (Model-based Analysis of ChIP-Seq) — the standard peak caller for ChIP-seq and ATAC-seq experiments. Identifies transcription factor binding sites (narrow peaks), histone modification domains (b

1 shared topic • 2 shared operations