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This article mainly shows you "how to use HECIL". The content is simple and easy to understand, and the organization is clear. I hope it can help you solve your doubts. Let Xiaobian lead you to study and learn this article "how to use HECIL".

HECIL(Hybrid Error Correction of Long Readings using Iterative Learning): This is a software based on the second generation data alignment, using iterative learning method to correct pacbio equal length read sequences.

1. software installation

Installation is relatively simple, download it from github.

git clone https://github.com/NDBL/HECIL.git cd HECIL#It is important that software and scripts have executable permissions. chmod +x bwa samtools Align_Corr.sh

If samtools, bwa depends on that package, you need to install the corresponding package yourself. For example, when I run bwa, I need to rely on "/lib64/libc.so.6". The solution is to download a new bwa and install it yourself.

2. Operation of software

The software is a Python script, so Python 2.7 is required to run.

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

Parameter Description:

-l : long sequence file, fasta format

-s: short sequence file, fastq format

-len: Length of short sequence

-o: Name of output directory

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