fixchr

Introduction

This package selects homologous chromosomes between two genomes by comparing whole-genome alignments between them. Additionally, it generates dotplots for quick checking of the output.

Installation:

The easiest method to install fixchr is using anaconda:

conda install -c bioconda fixchr    # TO BE DONE

For manual installation the pre-requisites are:

1. Python >= 3.8
2. Python libraries. These can be installed in a conda environment using:

   conda install numpy=1.21.2 pandas=1.2.4 matplotlib=3.3.4 setuptools pysam=0.19.0

   Then download fixchr and install:

   git clone https://github.com/schneebergerlab/fixchr.git
   cd fixchr
   python setup.py install

After this fixchr should be installed and in your environment. Test it by printing the help message:

fixchr -h

The package provides two binaries:

1. fixchr for filtering chromosomes
2. dotplot for visualising alignments using SAM/BAM/PAF/coord(from mummer) files

Inputs requirements

1. Chromosome-level assemblies for the genomes to be compared
2. Whole-genome alignment between them

Example command

fixchr -c alignment.paf -r ref.fa.gz -q qry.fa.gz -F P
dotplot -c alignment.paf -r ref.fa.gz -q qry.fa.gz -F P