ChromHMM: Chromatin state discovery and characterization
...lting model can then be used to systematically annotate a genome in one or more cell types. By automatically computing state enrichments for large-scale functional and annotation dat...2570 days ago
BEDOPS v2.4.26: high-performance genomic feature operations
...ity relationships between data sets. It aims to be scalable and flexible, facilitating the efficient and accurate analysis and management of large-scale genomic data. The overview s...2516 days ago
DIYA: a bacterial annotation pipeline for any genomics lab
DIY Genomics is an open source bioinformatics consortium intended to bring a collection of tools and libraries into the hands of small scale genomics labs for the process of sequence assembly and annotation. Projects include DIYA, MGAP, CRISPR, and DIYGV http://gmod.org/wiki/Diya2498 days ago
TRRUST v2: an expanded reference database of human and mouse transcriptional regulatory interactions
...egulatory relationships of 800 human TFs and 828 mouse TFs, respectively. They have been derived from 11,237 pubmed articles, which describe small-scale experimental studies of trans...2323 days ago
proovread : large-scale high-accuracy PacBio correction through iterative short read consensus
proovread : large-scale high-accuracy PacBio correction through iterative short read consensus outperforms PacBioToCA/LSC in terms of accuracy and contiguity/sensitivity (ht...2309 days ago
GIGGLE: a search engine for large-scale integrated genome analysis
...he significance of genomic loci shared between query features and thousands of genome interval files. GIGGLE (https://github.com/ryanlayer/giggle) scales to billions of intervals and...2304 days ago
MGcV: the microbial genomic context viewer for comparative genome analysis
MGcV is an interactive web-based visalization tool tailored to facilitate small scale genome analysis. To start using MGcV: Supply your genes/genomic segments/phylogenetic tree of...2285 days ago
GMOL: An Interactive Tool for 3D Genome Structure Visualization
GMOL was developed based upon our multi-scale approach that allows a user to scale between six separate levels within the genome. With GMOL, a user can choose any unit at any scale and scale it up or down to visualize its structure and retrieve corresponding genome sequences.2234 days ago
LACHESIS: Genome Assembly with Hi-C-based Contact Probability Maps (LACHESIS)
...t exploits contact probability map data (e.g. from Hi-C) for chromosome-scale de novo genome asse...Adey A, Patwardhan RP, Qiu R, Kitzman JO, Shendure J#. Chromosome-scale scaffolding of de novo genome...2180 days ago
fragScaff: Genome Assembly with Contiguity Preserving Transposition
...caffolding de novo genome assemblies. FragScaff is complementary to Lachesis, providing midrange contiguity to support robust, accurate chromosome-scale de novo genome assemblies wit...2180 days ago