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INTRODUCTION

CGAP-align is a read alignment package that is based on the Burrows-Wheeler Alignment tool (BWA). It mainly focus on optimizing the performance of the short read alignment component while remaining other part exactly the same.

SYNOPSIS¹

CGAP-align index database.fasta
either [CGAP-align optimize -w -s 200 database.fasta train.fa]
or [download the pre-built indices from our website]
CGAP-align aln -w database.fasta short_read.fastq > aln_sa.sai 
CGAP-align samse database.fasta aln_sa.sai short_read.fastq > aln.sam 

Click here to view all the pre-built indices.

Or, without DCDC:

CGAP-align index database.fasta
CGAP-align optimize database.fasta 
CGAP-align aln database.fasta short_read.fastq > aln_sa.sai 
CGAP-align samse database.fasta aln_sa.sai short_read.fastq > aln.sam 

USAGE

In this page, we only introduce the increamental commandlines introduced in CGAP-align w.r.t. short read alignment. For the other information, please refer to here. Please note that the data-conscious strategy(-w) might effect the output sai file which makes it different from that produced by BWA when aln -e is specified. BWA Plus will only find all the reads the ED of which is lower than -n while BWA will produce some extra reads that exceeds the limitation. In both case, no correctness problem is involved.

COMMANDS AND OPTIONS¹

CGAP-align optimize [options] \<ref.fa> [\<train.fa>]

Options:

-w index DFA tries enabling the data-conscious strategy to calculate width D-arrays. train.fa is required.
-s INT upper bound of the DFA trie size (MB) (MB)[200]
-h INT initial trie depth[45]
-t INT upper bound of the tree size (MB)

CGAP-align aln [options] \<prefix> \<in.fq>

Options:

-w use the data-conscious strategy to calculate width D-arrays. DFA tries index is required.

VERSIONS

0.1.1 Update bwa version to 0.6.1
0.1.0 Initial Version. Codebase: bwa 0.5.9

¹ For version 0.1.0, use "fpattern" instead of "optimize"