# mcutils

**Repository Path**: kylintu/mcutils

## Basic Information

- **Project Name**: mcutils
- **Description**: No description available
- **Primary Language**: Unknown
- **License**: Not specified
- **Default Branch**: master
- **Homepage**: None
- **GVP Project**: No

## Statistics

- **Stars**: 0
- **Forks**: 0
- **Created**: 2021-04-08
- **Last Updated**: 2021-04-08

## Categories & Tags

**Categories**: Uncategorized

**Tags**: None

## README

This is a set of tools I find helpful for working with whole genome
alignments stored in the SAM format.  Blasr (from this repository 
only: https://github.com/mchaisso/blasr ), and bwa-mem may both be
used to generate whole-genome alignments.

To build:

    cd src && make && make install

The blasr command is:

		sawriter target_genome.fasta
    blasr query_genome.fasta target_genome.fasta -alignContigs -maxAnchorGap 30000 -sam -minMapQV 30


The programs are:
+ samToBed - This version of a sam <-> bed converter allows the calculation of identity
+ samToDot - Create a file that may be rendered into a dotplot using RenderPlot.R
+ samLiftover - Transform coordinates from the query genome to target using the SAM file as a mapping.