nailpolish call

Consensus call duplicated reads The reads must first have been indexed.

Usage

$ nailpolish call --help
Generate a consensus-called 'cleaned up' file

Usage: nailpolish call [OPTIONS] --index <INDEX> --input <INPUT>

Options:
      --index <INDEX>          the index file
      --input <INPUT>          the input .fastq
      --output <OUTPUT>        the output .fasta; note that quality values are not preserved
  -t, --threads <THREADS>      the number of threads to use [default: 4]
  -d, --duplicates-only        only show the duplicated reads, not the single ones
  -r, --report-original-reads  for each duplicate group of reads, report the original reads along with the consensus
  -h, --help                   Print help

Output format

TODO

Options

• --duplicates-only: By default, nailpolish will consensus call all duplicated reads and also produces each non-duplicated read intact. With this flag, only the duplicated reads will be produced, and all non-duplicated reads will be skipped.
• --report-original-reads: By default, when reads are consensus called, only the consensus read is produced. With this flag, each of the original reads will be produced as well.