IGV (Integrative Genomics Viewer)

Fastq Screen — Perl tool for screening FASTQ sequencing reads against multiple reference genomes to detect sample contamination. Maps reads to user-defined genome databases (human, mouse, E. coli, Phi

2 shared topics • 2 shared operations

KneadData — quality control and host decontamination tool for metagenomic

2 shared topics • 2 shared operations

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

2 shared topics • 2 shared operations

Qualimap — platform-independent quality control tool for next-generation sequencing alignment data. Provides BAM QC (coverage, insert size, GC content, mapping quality), RNA-seq QC (gene body coverage

2 shared topics • 2 shared operations

REViewer — haplotype-resolved visualization of read alignments at short tandem repeat (STR) loci detected by ExpansionHunter. Accepts a sorted BAM/CRAM file, an ExpansionHunter VCF, a reference FASTA,

2 shared topics • 2 shared operations