Nathan Watson

v2.20

Python3 with numpy and scipy; base image: nathankw/centos6_essentials

Utilities for Stanford Genome Sequencing Service Center (GSSC) application logic on DNAnexus.

Creates a dsitrubtion of the barcodes present in the unmatched reads.

Extracts barcodes of interst from the unmatched reads into separate (paired-end) FASTQ files.

Extracts mate reads from FASTQ files.

Runs Trim Galore 0.4.1 and FASTQC 0.11.5.

RSEM knockdown expression plot for a given gene/transcript between control and treatment conditions.

NCBI BLAST+ v. 2.6.0 installed via NCBI's official rpm.

Python 2.7.14 compiled from source on top of the nathankw/centos6_essentials

Contains the pre-compiled binary of FASTX-Toolkit v. 0.0.13 from the Hannon Lab.

Base image is centos:centos6; adds tools needed to build and install other software.