The BaseSpace App store is rapidly growing with the release of six new Apps in the last two weeks. These include a new Isaac Whole Genome Sequencing App, ChIPSeq v1.0, String Graph Assembler App v1.0, a new version of the GENIUS Metagenomics: Know Now App, USC BedGraph Converter v1.0, and MiXCR Immune Repertoire Analyzer v1.1.
Isaac Whole Genome Sequencing v4.0
The App contains new and enhanced features that include the following:
- New structural variant (SV) caller
- New copy number variant (CNV) caller
- On node annotation for increased performance and stability
- Annotation of minor alleles that correspond to the reference genome (refminor)
- Ploidy Correction for Sex Chromosomes for small variants
- Variant quality score recalibration for small variant calling
- Isaac2 aligner (better performance and performs supplementary alignments)
- Merging of SV/CNV files to a single VCF file
- Bug and stability fixes
- Multi-node analysis (analyze up to 96 samples in parallel with each App launch)
Detailed information about about the App can be found in the application guide.
An example data set can be found here. In this example a HiSeq X run containing 16 whole human genomes at about 35X coverage was analyzed in about 8.5 hours. For comparison, the BWA/GATK App takes about 40 hours to complete on a single sample. The results contain fully annotated SNV and Indel calls as well as SV and CNV calls. In addition many of the software components found in the App have been made open source and are available for download from GitHub.
We also launched two BaseSpace Labs Apps.
The App uses MACS2 to identify enriched regions pulled down by chromatin immuno-precipitation, and HOMER to discover motifs within these regions. A sample data set is a available here. As shown below, the App contains an interactive peaks table that allows the user to quickly sort through the identified peaks and interrogate motifs associated with the peaks of interest. Note the interactive table may take up to a minute to load in some cases.
The second BaseSpace Labs App is the String Graph Assembler App v1.0.
String Graph Assembler v1.0
The String Graph is a method for de novo assembly of a genome sequence without using a reference genome. The String Graph Assembler (SGA) App is based on a software developed by Jared Simpson, formerly in Richard Durbin’s lab at the Wellcome Trust Sanger Institute in Cambridge, now a PI at the Ontario Institute for Cancer Research in Canada. This implementation has been shown to have a low memory footprint and is able to assemble medium-sized genomes including important model organisms such as C. Elegans and Drosophila within the limits of a Basespace virtual machine. Furthermore, the String Graph keeps all the information about reads and their overlaps in the input data and thus has advantages for the assembly of repetitive regions. The App also includes an installation of the BESST scaffolder written by Kristoffer Sahlin at the KTH Royal Institute of Technology in Stockholm, Sweden. The BESST scaffolder aligns all input reads to the contigs build by SGA and using read pairing information, joins the contigs into scaffolds. The BESST scaffolder supports paired-end and Nextera Mate Pair reads.
Finally, we launched three new third party Apps.
The first App is an update to the GENIUS Metagenomics: Know Now App.
Genius Metagenomics: Know Now App v1.1
This App supports analysis of shotgun metagenomics data and uses CosmosID’s curated genome database and offers bacterial identification at the species, subspecies, and/or strain level. The new version contains a tree view of the data.
The second App is USC BedGraph Converter v1.0 from the USC Keck School of Medicine.
USC BedGraph Converter v1.0
The App consumes bedGraph.gz output from any Basespace Application that produces bedGraph files. BedGraph.gz files are output from MethylSeq, TopHat, and RNA Express Apps. The App then converts bedgraph.gz files to bigwig which can be downloaded and used for IGV coverage plotting.
The third App is an immune repertoire sequencing App called MiXCR Immune Repertoire Analyzer v1.1.
MiXCR Immune Repertoire Analyzer v1.1
MiXCR is a universal software for processing of sequencing data from T- and B- cell receptor libraries. It aligns input reads on germline segments of Human or Mouse TRA, TRB, TRD, TRG, IGH, IGL, IGK genes, assembles clonotypes and corrects for PCR and sequencing errors. MiXCR was developed by Dmitriy Bolotin from the MiLaboratory at the Shemyakin-Ovchinnikov Institute of bioorganic chemistry RAS, Moscow, Russia and was recently described in a Nature Methods publication.
We now have 60 Apps in BaseSpace and provide analysis for most NGS sample types including WGS, Targeted DNA, RNASeq, Targeted RNA, small RNA, ChipSeq, MethylSeq, Metagenomics, and 16S. We will continue to work hard to bring the NGS community more high quality tools that are developed both internally as well as by our 3rd Party App partners.