The assembly graph can be large, complex and unwieldy, so DISCOVAR de novo does not generate a viewable graph directly. Instead we have developed an interactive tool that allows you to explore your assembly by creating smaller viewable graphs of the regions you are interested in. This new tool, called NhoodInfo, is now part of the DISCOVAR package, as of release 50612 . It is also the engine behind our online demo, so you can try it out right now without having to create an assembly of your own. Full instructions on using NhoodInfo are included in the DISCOVAR package.
We are pleased to announce the release of our new de novo assembler suitable for large genomes up to human size. This is an early release and should be considered experimental, but is fully functioning. Download it now.
Our new assembler, called DISCOVAR de novo (experimental), uses the same cheap data that the original DISCOVAR release does: 250 base paired-end PCR-free Illumina reads. No other libraries are required. The runtime for a human genome on a 48 core, 0.5 Tb server is only 36 hours, and produces an assembly with a contig N50 of ~100 kb.
We are actively developing DISCOVAR de novo, so check back often for updates.
DISCOVAR can now be freely used without restriction in both non-academic and academic settings under the terms of our new license. We still encourage users to register with us if they find DISCOVAR useful.
We’ve just added some examples to our online demo to help you explore our DISCOVAR de novo assembly of NA12878. You can select a region of interest from the new drop down menu and it will be displayed below. Alternatively, enter the coordinates of your favorite region of the genome if you want to explore on your own.
Want a sneak preview of what we’ve been working on lately? Then check out this online demo that lets you explore a de novo human assembly produced by our new assembler DISCOVAR de novo.
Developed over the past 6 months, the new DISCOVAR de novo algorithm will be released later this summer. Unlike DISCOVAR, it can assemble large genomes de novo. It is also much faster, but still takes the same low-cost single-library input data that DISCOVAR does.
Whilst we prepare DISCOVAR de novo for release, take a look at the online demo we’ve set up. Here you can explore and visualize an assembly of the human cell line NA12878. You can enter any coordinates on the human reference sequence GRCh38, and the demo will show you the part of the assembly that aligns there. Using this tool, large structural variation events can be directly visualized, and simple SNPs appear as short bubbles.
Please check it out and let us know what you think via the forum.
DISCOVAR now generates variant lists using the Variant Calling Format (VCF). This is the standard used by the community and is supported by many tools. Whilst the VCF file contains all events found by DISCOVAR, the complementary
.variant file may contain additional information not easily represented in the VCF format. We encourage our users to look at both. The VCF should be filtered prior to use, and we have provided a tool and instructions on how to do this.
To facilitate calling variants using DISCOVAR on large genomes, we have created a tool to merge VCF files generated for overlapping regions. Simply run DISCOVAR on each region in turn (or in parallel to speed things up), then merge the VCF files that are produced. We currently recommend using a 50 kb region size, with a 10 kb overlap.
For more information on the VCF output, filtering and merging, please refer to our manual.
Many people have asked if they can use their existing Illumina datasets with DISCOVAR – datasets that don’t meet the recommendations of ~60x coverage by 250 base paired reads from a ~450 bp PCR-free fragment library. We investigated and made some minor changes to the algorithm, embodied in release 46382 onwards, and it is now possible to use shorter reads from PCR libraries – with some caveats. We have successfully tested DISCOVAR on 100 base reads from a ~180 bp PCR fragment library, obtaining reasonable results but inferior to those generated from the recommended data. For more information on please see our FAQ.
A new release (r46399) of DISCOVAR is now available. It contains the following changes:
- More robust SAMtools version checking.
- Improvements to .variant file format.
- MALLOC_PER_THREAD = 1 environment setting no longer mandatory. However setting this may give a significant performance boost.
- Various bug fixes.
Thanks to all the users who have brought these problems to our attention.
We are pleased to announce that DISCOVAR is now available to download .
DISCOVAR is a variant caller and genome assembler from the Broad Institute. It uses the latest low cost sequencing data, and can generate highly accurate variant calls for individual humans, or assemble small genomes de novo (with support for large genomes to follow). We expect it will be particularly valuable for understanding human Mendelian disease, but equally suited to investigating the biology of other organisms.