Juicebox: Visualization and analysis software for Hi-C data
...s distribution includes the source code for Juicebox, Juicer Tools, and Assembly Tools. Download Juicebox here,...ki. Instructions below pertain primarily to usage of command line tools and the Juicebox jar files....1587 days ago
Best Practices for Variant Calling with the GATK
...03/19/15 Introduction to the GATK Geraldine Van der Auwera PDF Video 03/19/15 Mapping, processing, and duplicate marking with Picard tools Matt Sooknah PDF Video...1586 days ago
Dahak: benchmarking and containerization of tools for analysis of complex non-clinical metagenomes.
Dahak is a software suite that integrates state-of-the-art open source tools for metagenomic analyses. Tools in the dahak software suite will perform various steps in metagenomic analysis workflows...1539 days ago
HASLR: a hybrid assembler which uses both second and third generation sequencing reads
...e samples compared to other tested assemblers. Furthermore, the generated assemblies in terms of contiguity and accuracy are on par with the other tools on most of the samples. Avail...1514 days ago
Synteny and Rearrangement Identifier (SyRI)
...redicting genomic differences between related genomes using whole-genome assemblies (WGA). The assemblies are aligned using whole-genome alignment tools, and these alignments are the...1513 days ago
GRIDSS: the Genomic Rearrangement IDentification Software Suite
GRIDSS is a module software suite containing tools useful for the detection of genomic rearrangements. GRIDSS includes a genome-wide break-end assembler, as well as a structural vari...1501 days ago
Genobuntu: Package for Next Generation Sequencing and Genome Assembly
...ntaining more than 70 software and packages oriented towards NGS. In its current version, Genobuntu supports pre assembly tools, genome assemblers as well as post assembly tools.Commonly used biological soft...1500 days ago
1490 days ago
Liftoff: an accurate tool that maps annotations in GFF or GTF between assemblies
...accurate tool that maps annotations in GFF or GTF between assemblies of the same, or closely-related species. Unlike current coordinate lift-over tools which require a pre-generated...1457 days ago
merqury: Evaluate genome assemblies with k-mers
...of this read set can be used for independently evaluating assembly quality without the need of a high quality reference. Merqury provides a set of tools for this purpose. More at&nb...1454 days ago