pslMap / pslFilter

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

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

Nextclade — viral genome alignment, clade/lineage assignment, mutation calling, and sequence quality assessment. Aligns query sequences against pathogen-specific reference datasets (SARS-CoV-2, influe

1 shared topic • 2 shared operations

Purge Haplotigs — pipeline for curating heterozygous diploid genome assemblies by identifying and reassigning haplotigs (alternative haplotype contigs). Analyzes read-depth histograms to set coverage

1 shared topic • 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

1 shared topic • 2 shared operations