Description

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

Input

Name
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)

production_mode (boolean)

Whether to run in production mode (optional)

Output

Name
Description
Pattern

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

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.

versions_fcsgx

${task.process} (string)

The name of the process

fcsgx (string)

The name of the tool

gx --help | sed '/build/!d; s/.*:v//; s/-.*//' (eval)

The expression to obtain the version of the tool

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

Topics

Name
Description
Pattern

versions

${task.process} (string)

The name of the process

fcsgx (string)

The name of the tool

gx --help | sed '/build/!d; s/.*:v//; s/-.*//' (eval)

The expression to obtain the version of the tool

Tools

fcsgx Documentation

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

https://github.com/ncbi/fcs-gxdoi: 10.1186/s13059-024-03198-7License: NCBI-PD
Authors