Description

Runs FCS-GX (Foreign Contamination Screen - Genome eXtractor) to screen and remove foreign contamination from genome assemblies

Input

name:type
description
pattern

meta:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

taxid:string

Taxonomy ID of the expected organism

fasta:file

Input genome assembly file in FASTA format

*.{fa,fasta,fna}

gxdb:directory

Directory containing the FCS-GX database

ramdisk_path:string

Path to RAM disk for improved performance (optional)

Output

name:type
description
pattern

fcsgx_report

meta:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

*.fcs_gx_report.txt:file

Final contamination report with contaminant cleaning actions. Interpreted by gx clean genome to separate cleaned sequences from contaminants.

taxonomy_report

meta:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

*.taxonomy.rpt:file

Intermediate report with assigned taxonomies to individual sequences.

*.taxonomy.rpt

log

meta:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

*.summary.txt:file

FCSGX log file

*.summary.txt

hits

meta:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

*.hits.tsv.gz:file

Save intermediate alignments

*.hits.tsv.gz

versions

versions.yml:file

File containing software versions

versions.yml

Tools

fcsgx
NCBI-PD

The NCBI Foreign Contamination Screen. Genomic cross-species aligner, for contamination detection.

github.com/ncbi/fcs-gx github.com/ncbi/fcs/wiki https://github.com/ncbi/fcs-gx 10.1186/s13059-024-03198-7
maintainers
Github user tillenglert
Github user mahesh-panchal
get in touch
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