Jit
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BASE: a practical de novo assembler for large genomes using long NGS reads
By Rahul Nayak 2337 days agogithub.com - new de novo assembler called BASE. It enhances the classic seed-extension approach by indexing the reads efficiently to generate adaptive seeds that have high probability to appear uniquely in the genome. Such seeds form the basis for BASE...Platypus: A Haplotype-Based Variant Caller For Next Generation Sequence Data
By Shruti Paniwala 2331 days agowww.well.ox.ac.uk - Platypus is a tool designed for efficient and accurate variant-detection in high-throughput sequencing data. By using local realignment of reads and local assembly it achieves both high sensitivity and high specificity. Platypus can detect...Π-cyc: A Reference-free SNP Discovery Application using Parallel Graph Search
By Jit 1871 days agogithub.com - Reference free SNP search for comparative population genomics: multiple samples run simultanously. **experimental phase, compiles and runs with OpenMPI-1.8.8 with Intel Compiler only Cycles enumeration (aka Bubbles) as part of de novo de bruijn...D-GENIES: A tool for Dotplot large Genomes in an Interactive, Efficient and Simple way
By Jit 2467 days agodgenies.toulouse.inra.fr - D-GENIES – for Dotplot large Genomes in an Interactive, Efficient and Simple way – is an online tool designed to compare two genomes. It supports large genome and you can interact with the dot plot to improve the visualisation. We use minimap...karyoploteR: plot whole genomes with arbitrary data
By Abhimanyu Singh 2596 days agobernatgel.github.io - karyoploteR is an R package to create karyoplots, that is, representations of whole genomes with arbitrary data plotted on them. It is inspired by the R base graphics system and does not depend on other graphics packages. The aim of karyoploteR...VG: variation graph data structures, interchange formats, alignment, genotyping, and variant...
By Jit 1871 days agogithub.com - Variation graphs provide a succinct encoding of the sequences of many genomes. A variation graph (in particular as implemented in vg) is composed of: nodes, which are labeled by sequences and ids edges, which connect two nodes via either of...Ancestral Genomes: a resource for reconstructed ancestral genes and genomes across the tree of life
By Abhimanyu Singh 2323 days agoancestralgenomes.org - Ancestral Genomes (http://ancestralgenomes.org) is a resource for comprehensive reconstructions of these ‘fossil genomes’. Comprehensive sets of protein-coding genes have been reconstructed for 78 genomes of now-extinct species...kSNP3.0: SNP detection and phylogenetic analysis of genomes without genome alignment or reference...
By Jit 2652 days agosourceforge.net - Sept. 20, 2017 Version 3.1 released. Major upgrade. Version 3.1 fixes the problems with SNP annotation that arose when NCBI discontinued use of GI numbers. Please read carefully the Preface (page 3) and the File of annotated genomes section (pages...Tallymer: method to compute K-mer frequencies and its application to annotate large repetitive...
By Jit 2583 days agowww.zbh.uni-hamburg.de - Tallymer is based on enhanced suffix arrays. This gives a much larger flexibility concerning the choice of the k-mer size. Tallymer can process large data sizes of several billion bases. We used it in a variety of applications to study the...RefKA: A fast and efficient long-read genome assembly approach for large and complex genomes
By Rahul Nayak 1777 days agogithub.com - RefKA, a reference-based approach for long read genome assembly. This approach relies on breaking up a closely related reference genome into bins, aligning k-mers unique to each bin with PacBio reads, and then assembling each bin in parallel...
