Fastq-Join

Fastq-Join converts overlapping paired-end reads into longer fragment sequences.  It finds the overlap for each pair and combines them into a single read. This only works with paired ends with insert spacing shorter than approximately 2X the read lengths.

Quick Start

• To use Fastq-Join, enter the paired read files, a prefix name for the output files, and any options that are going to be set.
• Resources:http://code.google.com/p/ea-utils/wiki/FastqJoin

Test Data

Input File(s)

Use test_1.fastq and test_2.fastq from the directory above as test input.

Parameters Used in App

When the app is run in the Discovery Environment, use the following parameters with the above input file(s) to get the output provided in the next section below.

Use either the default parameters OR fill in the parameters -p, -m, -r, or -v, or combinations of these.

• • -p N    N-percent maximum difference (.20)

• • -m N    N-minimum overlap (6)
  • -r file   Verbose stitch length report
  • -v 'character'    Verifies that the 2 files probe id's match up to character. Use '/' for Illumina reads.

Output File(s)

Expect 3 sequence files as output (plus a report file, if a name for the report is entered). For the test case, the output files you will find in the example_data directory are named test20join, test20un1, test20un2.

Tool Source for App

• http://code.google.com/p/ea-utils/