assembly_alignment

Preliminary assembly-assembly alignment analysis

Features

• Creates a stats table with 1 row per assembly sequence with numbers per alignment discrepancy type
• Makes graphs, if the assembly has chromosomes
• Creates per assembly bed files for each discrepancy type

Future work

• Update stats to add the top ten by size for each even type

Install

Ensure you're using Python 2.7 and have bedtools installed, then:

$ git clone https://github.com/deannachurch/assembly_alignment
$ cd assembly_alignment

# Work around a pysam issue, https://github.com/pysam-developers/pysam/issues/247
$ export HTSLIB_CONFIGURE_OPTIONS="--disable-libcurl"

# Create a virtualenv and activate it
$ virtualenv env
$ source env/bin/activate

# Install dependencies
$ pip install -r requirements.txt

Run

Create a config file specifying path to files and files to create