16. Commonly used metagenomics tools
Here I’ve complied a (non-exhaustive) list of commonly used tools for analysing metagenomics data. As new tools are constantly being developed, it is likely that these tools will become outdated, but this will hopefully provide a great starting off point for further reading. Note that I’ve included tools for both short read (Illumina) and long read (Nanopore) data
Quality control and preprocessing of reads
- FASTQC
- fastp
- trimmomatic
- PRINSEQ
- nanoQC
- pycoQC
- LongQC
- NanoPack
- MultiQC
- Cutadapt
Read mapping
- BWA
- Bowtie2
- SOAP2
- GEM3
- Novoalign
- BBMap
- Minimap2
De novo metagenomic assemblers
- MEGAHIT
- metaSPADES
- IDBA-UD
- MetaVelvet
- OMEGA
- VICUNA
- SOAPdenovo2
- Canu
- metaFlye
- miniasm
- Wtdbg2
Genome/Contig binning
- DASTool
- MetaBat2
- MetaWRAP
- VAMB
- CONCOCT
- MaxBin
- GroopM
- MetaBinner
- MetaDecoder
- COMEBIN
- BASALT
- LRBinner
- MetaBCC-LR
Assembly quality control Tools
- MetaQUAST/QUAST
- DeepMAsED
- GenomeQC
- REAPR
- CheckM
- BUSCO
- EvalCon
- GUNC
- MAGISTA
- Bandage
Taxonomic identification Tools
- MetaPhlAn
- GTDB-TK
- Kraken2
- Bracken
- Centrifuge
- Kaiju
- DIAMOND
- MMseqs2
- BLAST
- Sourmash
- CLARK
- TaxMaps
- mOTUs2
- BugSeq
- GOTTCHA
- MetaCache
- MetaMaps
- MetaBit