Qualimap

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

3 shared topics • 2 shared operations

Graph-based alignment of reads to a population of genomes using hierarchical indexing — successor to TopHat and HISAT for RNA-seq alignment.

3 shared topics • 1 shared operation

Magic-BLAST — NCBI aligner for mapping large next-generation RNA or DNA sequencing runs against whole genomes or transcriptomes. Optimizes composite paired-read scores with splice-aware alignment, exc

3 shared topics • 1 shared operation

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,

3 shared topics • 1 shared operation

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

2 shared topics • 2 shared operations