Colormap-Project

The goal of this project is to re implement the methodology presented in the paper "CoLoRMap: Correcting Long Reads by Mapping short reads" by Ehsan Haghshenas, Faraz Hach, S. Cenk Sahinalp and Cedric Chauve

Dependencies

• Entrez Direct: used for downloading reference sequence NC 000913
  apt install ncbi-entrez-direct

• BWA - see here for installation : https://github.com/lh3/bwa. This code expects BWA to be in $PATH

• zlib.h
  apt-get install zlib1g-dev

• samtools
  apt install samtools

• Boost: C++ library used in the codebase to for store graphs,find connected components,run dijstra's shortest path etc.
  apt-get install libboost-graph-dev

• BLASR - used to align long reads to reference genome
  apt install -y blasr

Usage

Ecoli Data Initialization

To download the Illumina short reads, PacBio long reads and reference genome for the Escherichia coli str. K-12 substr. MG1655 do the following:
cd ecoli
bash init_ecoli.sh

Snakemake

Input:

The main 4 parameter for Snakefile are

1. folder: The name of the target folder which contains (ex. test_data/)
2. <short reads 1>.fastq: The name of one of fastq files in folder (ex. ill_1.fastq)
3. <short_reads_1>.fastq: The name of the other fastq file in folder (ex. ill_2.fastq)
4. <long reads>.fasta: The name of the fasta file in folder (ex. pac.fasta)

The other parameters are

• test_name: The suffix of the file containing the corrected long reads. More spefically, the corrected long reads will be stored in <folder>/lr_corr_<test_name>.fasta. This is an id that is intended to be used to distiguish the output files produced as the colormap.cpp is adjusted.
• correct_singletons: When set to "no", then a short read $s$ which has been mapped to a long read $l$ and is not adjacent to any other short reads mapped to $l$ will not be used to correct $l$. Other wise such short reads will be used to correct $l$

Output:

This pipeline produces the file

colormap.cpp

This file can be used directly to correct long reads. It takes 2 command line arguments:

1. <long_reads>.fasta
   this is just the relative path to the long reads which are
2. a "raw alignment file"