Karect

KAUST Assembly Read Error Correction Tool

Installation

tar -xzf file_name.tar.gz
cd karect
make

Instructions

To get all instructions, run the program:
./karect

Test Data and Running Example

Karect can accept as input any fasta/fastq file of assembly reads:
Running example used in the paper of correcting Staphylococcus aureus Illumina reads:

1. Download the files frag_1.fastq.gz and frag_2.fatstq.gz (and genome.fasta if you need to evaluate results) from:
   http://gage.cbcb.umd.edu/data/Staphylococcus_aureus/Data.original/

2. Decompress frag_1.fastq.gz and frag_2.fatstq.gz by:
   gunzip frag_1.fastq.gz
   gunzip frag_2.fastq.gz

3. Use Karect to correct the read sequences (modify file paths if needed):
   ./karect -correct -threads=12 -matchtype=hamming -celltype=haploid -inputfile=./frag_1.fastq -inputfile=./frag_2.fastq
   which produces the corrected read files: ./karect_frag_1.fastq and ./karect_frag_2.fastq

4. If you need to evaluate correction accuracy using the reference genome (genome.fasta):
   4a) First, align original reads to the reference genome, to produce the file ./align.txt
   ./karect -align -threads=12 -matchtype=hamming -inputfile=./frag_1.fastq -inputfile=./frag_2.fastq -refgenomefile=./genome.fasta -alignfile=./align.txt
   4b) Second, evaluate the correction accuracy to produce the file ./eval.txt
   ./karect -eval -threads=12 -matchtype=hamming -inputfile=./frag_1.fastq -inputfile=./frag_2.fastq -resultfile=./karect_frag_1.fastq -resultfile=./karect_frag_2.fastq -refgenomefile=./genome.fasta -alignfile=./align.txt -evalfile=./eval.txt

Author

Amin Allam
amin.allam@kaust.edu.sa

Reference

Currently submitted to Bioinformatics, under the title:
Karect: Accurate Correction of Substitution, Insertion and Deletion Errors for Next-generation Sequencing Data