Software download: RAUR.zip
RAUR is to re-align the reads that can not be mapped by alignment tools. It takes advantages of the base quality scores (reported by the sequencer) to figure out the longest segment of a read with at most K low quality bases. Combined with an alignment tool (like bwa or bowtie2), RAUR re-align the trimmed reads.
Author: Xiaoqing Peng
Contact: xqpeng@csu.edu.cn
Demands
The alignment tools bwa, bowtie2, and soap are properly installed, and the source codes of RAUR should be in the same folder with the executable files of bwa, bowtie2, and soap.
Usage
1. For paired-end reads:
perl Recurse_RAUR_pair.pl ref.fa read1.fq read2.fq read_flag aligner index
Parameters:
ref.fa The fasta file of referent genome
read1.fq One of fastq file of paired-end reads
read2.fq The other fastq file of paired-end reads
read_flag The header flag of these reads, like SRR, ERR
aligner 1 represents bwa algorithm, and 2 represents bowtie alogorithm
index 1 denotes index has exists, and 0 represents index is not exists yet.
Example:
perl Recurse_RAUR_pair.pl ref.fa ERR007641_1.filt.fastq ERR007641_2.filt.fastq ERR 1 1
2. For single-end reads:
perl Recurse_RAUR_pair.pl ref.fa read.fq read_flag aligner index
Parameters:
ref.fa The fasta file of referent genome
read1.fq The fastq file of paired-end reads
read_flag The header flag of these reads, like SRR, ERR
aligner 1 represents bwa algorithm, and 2 represents bowtie alogorithm
index 1 denotes index has exists, and 0 represents index is not exists yet.
Example:
perl Recurse_RAUR.pl ref.fa SRR006273.filt.fastq SRR 1 1