NAME

       atropos - NGS read trimming tool that is specific, sensitive, and speedy

SYNOPSIS

       atropos [--config <config file>] <command> [options]

OPTIONS

   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.

SEE ALSO

       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.

AUTHOR

       This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage
       of the program.

atropos 1.1.21                                     April 2019                                         ATROPOS(1)