ssu_finder

Identify SSU (16S/18S) rRNAs in sequences.

Identifies SSU (16S and 18S) rRNA genes residing on sequences, if these sequences are contained within a genome bin. A summary of the identified genes is written to <output_dir>/ssu_summary.tsv and their sequences to <output_dir>/ssu.fna.

Arguments

usage: checkm ssu_finder [-h] [-x EXTENSION] [-e EVALUE] [-c CONCATENATE] [-t THREADS] [-q]
                         seq_file bin_input output_dir

Identify SSU (16S/18S) rRNAs in sequences.

positional arguments:
  seq_file              sequences used to generate bins (fasta format)
  bin_input             directory containing bins (fasta format) or path to file describing genomes/genes - tab separated in 2 or 3 columns [genome ID, genome fna, genome translation file (pep)]
  output_dir            directory to write output files

options:
  -h, --help            show this help message and exit
  -x, --extension EXTENSION
                        extension of bins (other files in directory are ignored) (default: fna)
  -e, --evalue EVALUE   e-value threshold for identifying hits (default: 1e-05)
  -c, --concatenate CONCATENATE
                        concatenate hits that are within the specified number of base pairs (default: 200)
  -t, --threads THREADS
                        number of threads (default: 1)
  -q, --quiet           suppress console output

Example: checkm ssu_finder seqs.fna ./bins ./ssu_finder

Example

checkm ssu_finder seqs.fna ./bins ./ssu_finder