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NDBL / HECIL

Hybrid Error Correction of Long Reads using Iterative Learning
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HECIL

Hybrid Error Correction of Long Reads using Iterative Learning

Dependencies:

BWA (tested on version 0.7.15), Samtools (tested on version 0.1.18), Python (tested on version 2.7.8)

Running HECIL:

usage: python HECIL.py [-h] -l LR -s SR -len LENGTH_SR -o OUTPUT [-lc LOW_CONFIDENCE] [-c CUTOFF_QC] [-k CONFIDENCE_THRESHOLD]

Example command: python HECIL.py -l LongRead.fa -s ShortRead.fq -len 202 -o Out

The output containing all (corrected and uncorrected) long reads will be saved in LongRead_Corrected.fasta

Troubleshooting:

  1. If Align_Corr.sh, bwa, and samtools cannot execute after cloning the repository, run the following commands: chmod +x bwa chmod +x samtools chmod +x Align_Corr.sh

Contact: olivia.choudhury1@ibm.com