DNAnexus platform client libraries
Apps to build your app/applet/asset from source in a containerized environment.
C library for high-throughput sequencing data formats.
URL Fetcher: Fetch a file from a URL and upload it as a File.
Lightweight html5 version of the Integrative Genomics Viewer
Mongo DB Native NodeJS Driver
Style guides forked from those for Google-originated open-source projects
RNA-Seq Quality Control: Generates QC metrics for RNA-Seq data using the RSeQC suite; a graphical report of these metrics can be viewed on the DNAnexus website
GATK Pipeline: Recalibrates mapping qualities and calls variants using GATK
GATK Indel Realignment and Quality Recalibration: Deduplicates, realigns, and recalibrates a Mappings object in order to improve the quality of downstream variant calls, per the GATK best practices in variant detection.
GATK UnifiedGenotyper: Calls SNP and indel variations using GATK's UnifiedGenotyper.
Standards-compliant WebSocket client and server
RNA-Seq Analysis Pipeline: Maps RNA-Seq data and assesses expression using Tophat and Cufflinks
Pindel: Implements Pindel v.0.2.4t on mappings BAM files or Pindel input files
MediaWiki extension PdfExport
Client-side drafts MediaWiki extension
MediaWiki extension UploadLocal
BWA: Maps reads to a reference genome using the Burrows-Wheeler Aligner
Source code for some simple file-based applets
SAMtools mpileup: Variant calling for SNPs and Indels using SAMtools mpileup