Pore-C Tools

biobambam2 — C++ toolkit for early-stage BAM file processing built on libmaus2. Provides bamsormadup for parallel sorting with duplicate marking, bamcollate2 for name-collation, bammarkduplicates for

1 shared topic • 1 shared operation

Bismark — bisulfite-seq alignment and methylation calling toolkit. Maps bisulfite-treated reads to a reference genome using Bowtie 2, HISAT2, or minimap2, performs cytosine methylation calls in CpG/CH

1 shared topic • 1 shared operation

Bracken (Bayesian Reestimation of Abundance with KrakEN) — statistical method for computing species-level abundance estimates from Kraken/Kraken2/KrakenUniq taxonomic classifications. Redistributes re

1 shared topic • 1 shared operation

fastools — A Python-based toolkit by Jeroen F.J. Laros for the manipulation and characterization of FASTA and FASTQ files. Use when performing sequence conversions, filtering by length, generating seq

1 shared topic • 1 shared operation

featureCounts — ultrafast read counting program for assigning aligned reads (SAM/BAM) to genomic features such as genes, exons, promoters, and genomic bins. Part of the Subread package. Supports singl

1 shared topic • 1 shared operation