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.