mapseq
Description¶
Perform taxonomic classification of rRNA reads using reference databases
Pipelines¶
This module is used by the following pipelines:
Installation¶
nf-core modules -g https://www.github.com/ebi-metagenomics/nf-modules install mapseq
Tools¶
mapseq¶
Open source metagenomic 16S/18S read classifier enabling comparative metagenomics.
- github.com/jfmrod/MAPseq
- 10.1093/bioinformatics/btx517
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Input¶
| Name | Type | Description | Pattern |
|---|---|---|---|
meta |
map | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
- |
subunit_reads |
file | FASTA file containing rRNA gene reads | *.{fa,fasta} |
db_fasta |
file | Reference database FASTA file | *.{fa,fasta} |
db_tax |
file | Reference database OTU classifications file | *.txt |
db_mscluster |
file | Reference database OTU pre-clustering file | *.txt |
Output¶
| Name | Type | Description | Pattern |
|---|---|---|---|
meta |
map | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
- |
versions |
file | File containing software versions | versions.yml |
mseq |
file | Read classification output file | *.mseq |
