FCS adaptor input

Required inputs for run_fcsadaptor.sh:

• Genome sequence file: --fasta

• Taxonomy flag corresponding to source organism: --prok (prokaryote) or --euk (eukaryote)

• Usage: run_fcsadaptor.sh --help

Required inputs for fcs.py clean genome:

• Genome sequence file: --fasta

• FCS-adaptor report fcs_adaptor_report.txt: Final contamination report with contaminant cleaning actions.

• Usage: python3 fcs.py clean genome --help

Genome sequence file

The genome sequence file should be provided in FASTA format, optionally compressed with gzip. There is currently no support for running FCS-adaptor on FASTQ-formatted reads directly.

Definition lines

Each sequence in the file must have a definition line beginning with '>' and a unique identifier (SeqID), eg >contig001 or >contig002. The SeqIDs should:

• Be less than 50 characters long
• Only include letters, digits, hyphens (-), underscores (_), periods (.), colons (:), asterisks (*), and number signs (#).
• Be unique within a genome

Genome sequences

• All sequences must be more than 10 bp and less than 2 Gbp.
• No sequence should have >50% Ns.