lengths - SimonHegele/SSfSBT GitHub Wiki

Basic read length distribution analysis for one or multiple FASTA/FASTQ-files

usage: lengths [-h] [-c] [-s] [-p] [-t] files [files ...]

Basic read length distribution analysis.

positional arguments:
  files            FASTA/FASTQ-file(s)

options:
  -h, --help       show this help message and exit
  -c , --colors    Hexcodes for plotting
  -s , --scale     y-axis scale plots [default: linear]
  -p , --prefix    prefix for output-files [default: ssfsbt.lengths]
  -t , --threads   number of parallel threads to use for counting [default: 1]

Examplary output:

Example plot

            File  # Sequences     # Bases  Min len  Mean len  Max len  Std
0    halc.fasta      1000000  1464965219      141      1464    10655  932
1  halc_s.fasta      1154199  1275200520      100      1104     5937  850
2  halc_t.fasta       999867  1348884260       14      1349     8322  885