nmdp-bioinformatics/ngs

Name: ngs

Owner: NMDP/Be The Match Bioinformatics Research

Description: Next generation sequencing (NGS/HTS) tools.

Created: 2014-09-11 16:43:25.0

Updated: 2018-01-09 05:35:48.0

Pushed: 2017-11-13 08:39:26.0

Homepage:

Size: 9794

Language: Java

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README

ngs

Next generation sequencing (NGS/HTS) tools.

Using ngs

Artifacts from this project are available from the Maven Central repository.

E.g.

endency>
roupId>org.nmdp.ngs</groupId>
rtifactId>ngs-align</artifactId>
ersion>${version}</version>
pendency>

• Maven Central artifact search
• Javadoc documentation for latest release

Using ngs-tools

The ngs-tools module builds several command line tools.

For example

s-downsample-fastq -h
e:
downsample-fastq -p 0.5 [args]

ments:
a, --about  display about message [optional]
h, --help  display help message [optional]
i, --input-fastq-file [class java.io.File]  input FASTQ file, default stdin [optional]
o, --output-fastq-file [class java.io.File]  output FASTQ file, default stdout [optional]
p, --probability [class java.lang.Double]  probability a FASTQ record will be removed, [0.0-1.0] [required]
z, --seed [class java.lang.Integer]  random number seed, default relates to current time [optional]

Hacking ngs

Install

• JDK 1.7 or later, http://openjdk.java.net
• Apache Maven 3.2.5 or later, http://maven.apache.org

To build

$ mvn install