Compute the entire distributions of as_read strand lengths for given flow cells and channels, in a set of input SMS files. lengthToolLite is similar to lengthTool, but does not calculate as_aligned length. Forgoing alignments can provide useful information with much less computation across the entire data set.

$ lengthToolLite --in_file reads.sms

Generic options:
  --help                Produce help message

Required options:
  -i [ --in_file ] arg  Read file name (sms)

Optional options:
  --flow_cells arg (=1-2) flowcells to process
  --channels arg (=1-25)  channels to process
  --pass arg (=1)         pass to process (1 or 2)
  --prefix arg            Prefix for output files
  --force                 Force output files

lengthToolLite outputs two files. The first is named based on the flowcell and channel numbers (length.as_read.summary.fcX.chX). It contains the as_read read length distribution for a specific flowcell/channel.

The second file, yield.summary.txt, lists the total number of reads and the mean read length seen per input file for each channel and flow cell encountered during lengthToolLite execution across all input file (if an input file did not contain data for a particular flow cell/channel, then the number of reads will be 0 and the mean length will be nan). Only one yeild.summary.txt file is output per invocation of lengthToolLite.