catpack_contigs

Description

Taxonomic classification of long DNA sequences and metagenome assembled genomes (e.g. contigs, MAGs / bins).

Keywords: taxonomic classification, classification, long reads, mags, assembly

Installation

ebi-metagenomics/catpack/contigs

nf-core modules -g https://www.github.com/ebi-metagenomics/nf-modules install catpack/contigs

Tools

catpack

CAT/BAT: tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs)

• github.com/MGXlab/CAT_pack
• 10.1186/s13059-019-1817-x
• github.com/MGXlab/CAT_pack
• MIT

Input

Name	Type	Description	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]	-
contigs	file	A nucleotide FASTA file containing long DNA sequences such as contigs.	*.{fasta,fna,fa,fas}
meta2	map	Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]	-
database	directory	Directory containing CAT_pack database files (e.g. output from CAT_pack prepare)	*/
meta3	map	Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]	-
taxonomy	directory	Directory containing CAT_pack taxonomy files (e.g. output from CAT_pack prepare)	*/
meta4	map	Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]	-
proteins	directory	Optional pre predicted-made proteins FASTA	*.{fasta,faa,fa,fas}
meta5	map	Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]	-
diamond_table	directory	Optional pre-made DIAMOND alignment table	*

Output

Name	Type	Description	Pattern
orf2lca	file		-
contig2classification	file		-
log	file		-
diamond	file		-
faa	file		-
gff	file		-
versions	file		-

People

Authors

• @jfy133

Maintainers

• @jfy133