Active projects

NGS data analysis

ngsutilsj

Updated NGS data processing toolkit. Programs for working with FASTQ, FASTA, BAM, VCF, BED, GTF, and tab-delimited text annotation files. (active development)

Java

cgsplice

Splicing analysis toolkit. Used for finding novel splice junctions and differential splicing analysis.

Java

swalign

Smith-Waterman local alignment library/tool

Python 2/3

Pipeline definition and execution

cgpipe

Language for defining and running pipelines on HPC clusters

Java

SBS

Single user batch job scheduler for workstations

Python 2

Misc. tools/libraries

tabl

Program for viewing and working with tab-delimited text files (and CSV).

Go

kdpeaks

Find peaks in kernel density estimate (KDE) matrices

R

compgen-common

Common utility classes useful for Java projects

Java-library

compgen-cmdline

Framework for developing Java command-line applications that have a *nix feel

Java-library

Older tools

NGSUtils

Original NGS data processing toolkit (maintenance only)

Python 2

tabutils

Utility progams for working with tab-delimited text files

Python 2

basespace-download

Download files / samples from Illumina's BaseSpace

Go