Port of the Makeflow Hecil workflow to HyperFlow.
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.
Use the Docker container image hyperflowwms/hecil-worker, or build it yourself:
make image
If you do not have real data to work with, then generate some simulated data (~10 second workflow):
./scripts/fastq_generate.pl 100000 1000 > ref.fastq
./scripts/fastq_generate.pl 10000 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
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).