atropos - NGS read trimming tool that is specific, sensitive, and speedy
atropos [--config <config file>] <command> [options]
- detect:
- Detect adapter sequences directly from read sequences. Use
this command if you are unsure if your data has adapters, or if you know
that it has adapters but you don't know what are the adapter
sequences.
- error:
- Estimate the sequencing error rate. Use this command to
help determine the quality of your data, and to decide the value for the
max error rate ( -e) parameter. Normal error for an Illumina
experiment is around 1% or less. We recommend setting -e to 10x the
empirical error rate.
- qc:
- Compute read-level statistics. The output is identical to
running the 'trim' command with '--stats pre'. Use this command to get an
idea of the quality of your raw data.
- trim:
- Trim adapters and low-quality bases, and perform other NGS
preprocessing. This command provides most of Atropos' functionality.
-
-h, --help
- show this help message and exit
-
--config <config file>
- provide options in a config file
Use "atropos <command>
--help" to see all options for a
specific command. See
http://atropos.readthedocs.org/ for full documentation.
Atropos is a fork of Cutadapt 1.10 (
https://github.com/marcelm/cutadapt/tree/2f3cc0717aa9ff1e0326ea6bcb36b712950d4999)
by John Didion, et al., "Atropos: sensitive, specific, and speedy
trimming of NGS reads, submitted.
Cutadapt (
https://github.com/marcelm/cutadapt) was developed by Marcel Martin,
"Cutadapt Removes Adapter Sequences From High-Throughput Sequencing
Reads," EMBnet Journal, 2011,
17(1):10-12.
This manpage was written by Andreas Tille for the Debian distribution and can be
used for any other usage of the program.