Nextclade

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

GATK HaplotypeCaller — germline short variant caller using localized de novo assembly of haplotypes. Calls SNPs and indels from BAM/CRAM alignment files, producing VCF or gVCF output. Supports single-

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

OrthoFinder — fast, accurate ortholog inference for comparative genomics. Identifies orthogroups, orthologs, gene trees, rooted species trees, and gene duplication events from protein or nucleotide se

1 shared topic • 2 shared operations