MetaMaps

bamAlignCleaner — removes unaligned references from BAM/CRAM alignment files. Cleans alignment files by filtering out reference sequences with no mapped reads, reducing file size and speeding downstre

1 shared topic • 1 shared operation

Bowtie2 — ultrafast and memory-efficient short-read aligner using FM-index with gapped alignment and local alignment modes. Standard aligner for ChIP-seq, ATAC-seq, CUT&RUN, CUT&Tag, and general short

1 shared topic • 1 shared operation

DAS Tool — genome-resolved metagenomics bin refinement tool that integrates results from multiple binning algorithms to produce an optimized, non-redundant set of metagenome-assembled genomes (MAGs).

1 shared topic • 1 shared operation

EMU (Exact Mapping-based Unambiguous) — species-level 16S rRNA taxonomic profiling for long-read sequencing data (Oxford Nanopore, PacBio). Uses an expectation-maximization algorithm to resolve multi-

1 shared topic • 1 shared operation

Kraken 2 — fast k-mer-based taxonomic sequence classifier for metagenomics. Assigns NCBI taxonomic labels to DNA/protein sequences using exact k-mer matching against a minimizer-indexed hash table. Su

1 shared topic • 1 shared operation