commands¶

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.

optional arguments¶

-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.