trajectoread source

Overview

Source contains source files of DNAnexus Apps developed to process Illumina reads data. These applets are used in the processing and delivery of sequencing reads data generated from Illumina sequencing platforms.

Functions

• Curate data with multi-dimensional metadata
• Use the following metadata types to make data searchable * Details: Fixed key-value pairs used to describe data provenance * Properties: Mutable key-value pairs that describe data to be used by downstream analyses * Tags: Mutable strings that tag data with phrases useful to end-users
• Use a standard dictionary for storing metadata

Value

• Make it easy to find relevant data for downstream analyses
• Allow users to quickly generate sophisticated profiles of large data pools
• Allow users to do fine-grained data searching/filtering
• Describe & maintaing data provenance

Files

SCGPM Bcl2fastq

• dxapp.json: DNAnexus app configuration file.
• src/code.py: DNAnexus app source code.
• resources: Illumina Bcl2fastq binary.

Getting Started

1. Clone the trajectoread_source repo to your local or remote machine

git clone https://github.com/StanfordBioinformatics/trjread-source.git
cd trjread-source

2. Install and configure the DNAnexus software development kit (dx-toolkit). https://wiki.dnanexus.com/Downloads

3. Build as an applet using dx-toolkit.

dx build scgpm_bc2lfastq

4. You can also use the trjread-builder module to deploy this applet in stand-alone form or as part of workflow. Instructions for using trjread-builder can be found here: https://github.com/StanfordBioinformatics/trjread-builder.

python builder.py -e production -a bcl2fastq2_by_lane