featureCounts

bwa-meth -- fast and accurate bisulfite-seq (WGBS/RRBS) aligner built on BWA-MEM. Performs in-silico C-to-T conversion of reads and reference, aligns with BWA-MEM or BWA-MEM2, and recovers original ba

1 shared topic • 2 shared operations

Sailfish — rapid mapping-based isoform quantification from RNA-seq reads. Uses quasi-mapping to estimate transcript abundance without full alignment. Provides TPM and estimated counts per transcript.

1 shared topic • 2 shared operations

Sarek — nf-core Nextflow pipeline for germline and somatic variant calling from whole-genome sequencing (WGS), whole-exome sequencing (WES), and targeted sequencing data. Supports multiple variant cal

1 shared topic • 2 shared operations

SortMeRNA — fast filtering of ribosomal RNA reads from metatranscriptomic and RNA-seq data using local sequence alignment against curated rRNA databases (SILVA, RFAM). CLI tool for rRNA removal, rRNA

1 shared topic • 2 shared operations

vt — C++ command-line variant tool set for manipulating VCF files. Provides variant normalization (left-alignment and trimming), multiallelic decomposition, VCF summary statistics (peek), annotation,

1 shared topic • 2 shared operations