Guppy

BBDuk (Decontamination Using Kmers) — high-performance Java tool from the BBTools suite for adapter trimming, quality trimming, contaminant filtering, sequence masking, GC filtering, and format conver

2 shared topics • 2 shared operations

EAGER2 / nf-core/eager — reproducible Nextflow pipeline for ancient DNA (aDNA) and palaeogenomics. Handles adapter trimming with AdapterRemoval2, read merging, low-complexity filtering, mapping with B

2 shared topics • 2 shared operations

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 • 1 shared operation

MetaWRAP — flexible pipeline for genome-resolved metagenomic data analysis. Wraps read QC (trimming, host removal), metagenomic assembly (MEGAHIT, metaSPAdes), binning (MaxBin2, metaBAT2, CONCOCT), bi

2 shared topics • 1 shared operation

methylpy — Python pipeline for whole-genome bisulfite sequencing (WGBS) methylation analysis. Trims adapters, aligns with Bowtie2, marks duplicates, and calls cytosine methylation in CpG, CHG, and CHH

2 shared topics • 1 shared operation