Mask Dna

Summary

Mask an input fasta file for sequences that could be RNA viral (or mistaken for such).

Description

Mask an input fasta file for sequences that could be RNA viral (or mistaken for such).

Usage

rolypoly mask-dna [OPTIONS]

Options

• -t, --threads: Number of threads to use (type: INTEGER; default: 1)
• -M, --memory: Memory in GB (type: TEXT; default: 6gb)
• -o, --output: Output file name (type: TEXT; required; default: Sentinel.UNSET)
• -f, --flatten: Attempt to kcompress.sh the masked file (type: BOOLEAN; default: False)
• -i, --input: Input fasta file (type: TEXT; required; default: Sentinel.UNSET)
• -a, --aligner: Which tool to use for identifying shared sequence (minimap2, mmseqs2, diamond, bowtie1, bbmap) (type: TEXT; default: mmseqs2)
• -mlc, --mask-low-complexity: Whether to mask low complexity regions using bbduks entropy masking (type: BOOLEAN; default: False)
• -r, --reference: Provide an input fasta file to be used for masking, instead of the pre-generated collection of RNA viral sequences (type: TEXT; default: /clusterfs/jgi/scratch/science/metagen/neri/code/rolypoly/data/contam/masking/combined_entropy_masked.fasta)
• --tmpdir: Temporary directory to use (default: output file's parent/tmp - if you have enough RAM, you can set this to /dev/shm/ or /tmp/ for faster I/O) (type: TEXT)