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 Corrected_LongRead.fa
Troubleshooting:
- 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: [email protected]