Scripts

Scripts

A list of tools provided by Hagfish

All Hagfish scripts will give you an overview of command line parameters if you run the script with -h or --help.

Hagfish consists of the following scripts:

• hagfish_extract

  Perform the inital data extraction for hagfish from the input BAM files. Hagfish extract reads the BAM files, estimates the insert size (check this!), and writes per-bam per-sequence coverage plots.

• hagfish_coverage_combined

  Combines the per-bam-per-sequence coverage plots into one coverage plot per sequence subsequent use by Hagfish.

• hagfish_flatten

  Generate a (flat) gff file indicating what regions of a sequence are 'good', 'uncertain' or 'bad'.

• hagfish_report

  Generate a simple report and a cumulative coverage plot - indicating the overall coverage of the reference genome.

• hagfish_cplot

  Create stacked pseudo-coverage plots per sequence

• hagfish_blockplot

  generate a 'blockplot' - badly named - generates a pseudo-color plot of the hagfish error score showing the quality of the alingment in that specific position

There are a few more scripts - considered experimental. Use at your own risk (well, to be precise - use everything at your own risk)