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BAMtools — C++ API and command-line toolkit for reading, writing, sorting, indexing, filtering, merging, splitting, and converting BAM alignment files. Provides JSON-based filter expressions, multi-fo

2 shared topics • 2 shared operations

DADA2 — high-resolution amplicon sequence variant (ASV) inference from Illumina, 454, and Ion Torrent amplicon sequencing data. R/Bioconductor package that models sequencing errors to resolve exact bi

2 shared topics • 2 shared operations

HiCUP (Hi-C User Pipeline) is a modular pipeline for mapping and performing quality control on Hi-C sequencing data. Processes paired-end FASTQ reads through four stages: truncation at ligation juncti

2 shared topics • 2 shared operations

LotuS2 (Less OTU Scripts 2) — ultrafast amplicon sequencing pipeline for 16S, 18S, 23S, 28S, and ITS marker gene analysis of microbial communities. Processes raw FASTQ/FASTA through demultiplexing (sd

2 shared topics • 2 shared operations

Pychopper — Nanopore direct cDNA read preprocessing tool that identifies, orients, and trims full-length reads using primer detection (pHMM or alignment). Rescues fused reads by dynamic programming, e

2 shared topics • 2 shared operations