Skip to content

Software and references used in this pipeline

Software packages

FastP Version 0.24, doi: 10.1093/bioinformatics/bty560, PubMed github

MultiQC Version 1.22, doi: 10.1093/bioinformatics/btw354, PubMed github

Vsearch Version 2.27.0, doi: 10.7717/peerj.2584, PubMed github

Cutadapt Version 4.6, doi: 10.14806/ej.17.1.200, Embnet github

Dada2 Version 1.30, doi: 10.1038/nmeth.3869 , PubMed github

Blast+ Version 2.14.1, doi: 10.1016/S0022-2836(05)80360-2, PubMed ftp

Nanofilt Version 2.8.0, doi: 10.1093/bioinformatics/bty149, PubMed github

Nanoplot Version 1.41.6, doi: 10.1093/bioinformatics/btad311, PubMed github

Porechop ABI Version 0.5.0, BioRxiv github

References

Midori References used by this pipeline are obtained from the Midori database, based on GenBank release 2023-12-17.

Version 2023-12, 17, doi: 10.1093/bioinformatics/bty454, Pubmed

Unite Reference database for ITS sequences Unite

Version 10.0, doi: 10.1093/nar/gkad1039 PubMed