Tools for Assembly Analysis

Contents

• asmToRefViz.py
• Contigous_alignment.py

asmToRefViz.py

This script produces a visualization of alignments from a sam, bed, or paf file to the associated reference.
Input: alignment file (.sam, .bed, .paf), reference file (.fa or .fai)
Output: .png file showing alignments

usage: asmToRefViz.py [-h] --outpath OUTPATH --inpath INPATH [INPATH ...] (--ref REF | --ref_fai REF_FAI) [--contig_cutoff CONTIG_CUTOFF] [--color COLOR [COLOR ...]] [--size SIZE SIZE] [--fontsize FONTSIZE]

optional arguments:
-h, --help
   show this help message and exit
--outpath OUTPATH, -o OUTPATH
   Path for saving .png file
--inpath INPATH [INPATH ...], -i INPATH [INPATH ...]
   File paths for asm comparisson
--ref REF
   Path to reference file, this will create an .fai file
--ref_fai REF_FAI
   Path to .fai file for reference
--contig_cutoff CONTIG_CUTOFF
   Filter out all contigs smaller than this value
--color COLOR [COLOR ...], -c COLOR [COLOR ...]
   RGBA color values seperated by , and a space between colors ex. 156,156,128,256 212,10,15,256 The number of colors should
   match the number of assemblies
--size SIZE SIZE, -s SIZE SIZE
   xsize ysize
--fontsize FONTSIZE, -f FONTSIZE
   Font size, the larger the number of contigs the smaller you should go.

Contigous_alignments.py

This script filters reads based on a variety of parameterized contiguity measures
Input: alignment file (.sam)
Output: filtered alignment file (.sam)

usage: Contigous_alignment.py [-h] --output OUTPUT [--supplementary_output SUPPLEMENTARY_OUTPUT] --input INPUT [INPUT ...] [--min_coverage MIN_COVERAGE] [--max_insertion MAX_INSERTION] [--max_deletion MAX_DELETION] [--max_softclip MAX_SOFTCLIP] [--max_hardclip MAX_HARDCLIP]

optional arguments:
-h, --help
   show this help message and exit
--output OUTPUT, -o OUTPUT
   Path to desitnation output bed file
--supplementary_output SUPPLEMENTARY_OUTPUT, -so SUPPLEMENTARY_OUTPUT
   Optional output for regions deemed not covered
--input INPUT [INPUT ...], -i INPUT [INPUT ...]
   Any number of input sam paths, must be for same reference
--min_coverage MIN_COVERAGE, -m MIN_COVERAGE
   The minimum number of contigous reads to count as observed.
--max_insertion MAX_INSERTION
   The maximum size of a single insertion event in a given SAM alignment.
--max_deletion MAX_DELETION
   The maximum size of a single deletion event in a given SAM alignment.
--max_softclip MAX_SOFTCLIP
   Maximum allowable size for softclip
--max_hardclip MAX_HARDCLIP
   Maximum allowable size for hardclip