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CABOG: Celera Assembler with Best Overlap Graph
By Abhimanyu Singh 3370 days agowww.jcvi.org - CABOG (Celera Assembler with Best Overlap Graph) is scientific software for DNA research. CABOG has been a critical component of many genome sequencing projects. CABOG operates on small genomes such as bacterial as well as large genomes such as...RATT
By Jitendra Narayan 3833 days agoratt.sourceforge.net - RATT is software to transfer annotation from a reference (annotated) genome to an unannotated query genome. It was first developed to transfer annotations between different genome assembly versions. However, it can also transfer annotations between...Redundans
By Jit 3626 days agogithub.com - Redundans pipeline assists an assembly of heterozygous genomes.Program takes as input assembled contigs, paired-end and/or mate pairs sequencing libraries and returns scaffolded homozygous genome assembly, that should...ScaffMatch
By Jit 3523 days agoalan.cs.gsu.edu - caffMatch is a novel scaffolding tool based on Maximum-Weight Matching able to produce high-quality scaffolds from NGS data (reads and contigs). The tool is written in Python 2.7. It also includes a bash script wrapper that calls aligner in case one...Salzberg lab
We are a computational biology lab that develops novel methods for analysis of DNA and RNA sequences. Our research includes software for aligning and assembling RNA-seq data, whole-genome assembly, and microbiome analysis. We work closely with...LACHESIS: Genome Assembly with Hi-C-based Contact Probability Maps (LACHESIS)
By Jit 3006 days agoshendurelab.github.io - LACHESIS is method that exploits contact probability map data (e.g. from Hi-C) for chromosome-scale de novo genome assembly. Further information about LACHESIS, including source code, documentation and a user's guide are available...Jvarkit : Java utilities for Bioinformatics
By Jit 2981 days agolindenb.github.io - Collection of Java tool kits for bioinformatics works: Jvarkit : Java utilities for Bioinformatics
Structural variants PPT
By Jit 3620 days ago1000 Genomes data tutorial at ASHG Structural variants presentation by Jan Korbel European Molecular Biology Laboratory (EMBL) Heidelberg Genome Biology Research...CANU: Assembling Large Genomes with Single-Molecule Sequencing and Locality Sensitive Hashing.
By Jit 3754 days ago Comments (2)github.com - Canu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing (such as the PacBio RSII or Oxford Nanopore MinION). The software is currently alpha level, feel free to use and report issues encountered. Canu is...GAGE : Genome Assembly Gold-standard Evaluation
By Jit 3620 days agogage.cbcb.umd.edu - GAGE is an evaluation of the very latest large-scale genome assembly algorithms. We have organized this "bake-off" as an attempt to produce a realistic assessment of genome assembly software in a rapidly changing field of next-generation sequencing....
