Downsample reads

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Reduce the number of reads in fastq or fasta files to reduce overload of an assembler.

Quick Start

To use Downsample reads, import your data in fastq format.
Resources: http://hannonlab.cshl.edu/fastx_toolkit/commandline.html#fastx_collapser_usage

Test Data

Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> downsample_reads

Input File(s)

Use:

wt1.fq

wt2.fq

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.

Default parameters only, except change unpaired to paired reads.

Output File(s)

Expect a as output files named after the input files. For the test case, the output files you will find in the example_data directory are named:

dwn_smpl_wt1.fq

dwn_smpl_wt2.fq

Tool Source for App

http://hannonlab.cshl.edu/fastx_toolkit/commandline.html#fastx_collapser_usage