Duke Center for Genomic and Computational Biology

CWL on Kubernetes

iMADS API client that generates on-demand predictions using Docker and CWL

Web portal and supporting services that allow searching/creating TF predictions and preferences.

Production apache setup for iMADS website.

R Script for generating TF binding preferences from libsvm predictions

Code for modeling and predicting TF-DNA binding using libsvm

Picard, based on broadinstitute/picard, customizing CMD

seqtk installed via apt

Dependencies (Java, R) for running GATK

Babraham Bioinformatics - Trim Galore!

BWA image with samtools for BAM output

BWA: Burrow-Wheeler Aligner for pairwise alignment between DNA sequences

SeekDeep ubuntu-based image

Docker image for SPP

Tools (written in C using htslib) for manipulating next-generation sequencing data

Software for predicting library complexity and genome coverage in high-throughput sequencing.