Skip to content

Latest commit

 

History

History

hecil

README.md

HECIL Workflow Example

This workflow gives an example of using Makeflow to parallelize the Hybrid Error Correction with Iterative Learning (HECIL) tool.

Citation: "HECIL: A Hybrid Error Correction Algorithm for Long Reads with Iterative Learning", Olivia Choudhury, Ankush Chakrabarty, and Scott Emrich bioRxiv preprint, 2017. https://doi.org/10.1101/162917

The conversion of HECIL into a workflow was accomplished by Connor Howington as part of a summer REU project at Notre Dame.

Installation and Use

Before beginning, make sure you have already cloned the makeflow-examples repository and are in the hecil directory:

git clone https://github.com/cooperative-computing-lab/makeflow-examples
cd makeflow-examples/hecil

First, build the bwa binary for your architecture:

git clone https://github.com/lh3/bwa bwa-src
cd bwa-src
make
cp bwa ..
cd ..

git clone https://github.com/samtools/htslib htslib --branch 1.15.1
cd htslib
git submodule update --init --recursive
autoreconf
make
cd ..

git clone https://github.com/samtools/samtools samtools-src --branch 1.15.1
cd samtools-src
autoreconf
make
cp samtools ..
cd ..

If you do not have real data to work with, then generate some simulated data, which will result in a ~15 minute workflow on a single machine:

./fastq_generate.pl 100000 1000 > ref.fastq
./fastq_generate.pl 100000 100 ref.fastq > query.fastq

The long read file needs to be in fasta format, so you'll need to convert it:

./convert_fastq.py ref.fastq > ref.fasta

Then, generate a workflow to process the data:

./make_hecil_workflow -l ref.fasta -s query.fastq -len 100 -p 100 -ps 2 -rs 1000

Finally, execute the workflow using makeflow locally or using a batch system like Condor, SGE, or Work Queue:

makeflow hecil.mf
makeflow -T condor hecil.mf
makeflow -T sge hecil.mf
makeflow -T wq hecil.mf

Alternatively, it can be run using the JX or JSON representation

makeflow --jx hecil.jx
makeflow --json hecil.json

corr.out (default) contains only the corrected long reads. Corrected_ref.fasta contains all reads, with the corrected reads replacing the old reads (order is not conserved from input fasta file).