Jit
Enthusiast computational biologist with business dream !!!
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CANU: Assembling Large Genomes with Single-Molecule Sequencing and Locality Sensitive Hashing.
By Jit 3131 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...SALSA: A tool to scaffold long read assemblies with Hi-C
By Jit 2351 days agogithub.com - This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branch. To use the latest version,...CGView.js is a Circular Genome Viewing tool
By LEGE 239 days agohttps://js.cgview.ca/ - CGView.js is a Circular Genome Viewing tool for visualizing and interacting with small genomes. This software is an adaptation of the Java program CGView. CGView.js is the genome viewer of Proksee, an expert system for genome...Public Databases for Bioinformatics !
By Jit 1339 days agomitra.stanford.edu - https://www.nature.com/articles/s41467-020-17155-yServer Infrastructure: File Server: dhara: Synology 3614 Storage Appliance 4 Core Xeon 108TB disk storage 10Gb ethernet to SCG3 Access atx: dhara:5000 Has btsync server (try it - its much...Ribbon: Visualizing complex genome alignments and structural variation:
By Jit 2549 days agohttp://genomeribbon.com/ - Ribbon can be used for long reads, short reads, paired-end reads, and assembly/genome alignments. Instructions for each data format are available by clicking on "instructions" in each tab on the right. Local installation: You can install Ribbon...Mash: fast genome and metagenome distance estimation using MinHash
By Jit 2536 days agogithub.com - Mash is normally distributed as a dependency-free binary for Linux or OSX (see https://github.com/marbl/Mash/releases). This source distribution is intended for other operating systems or for development. Mash requires c++11 to build, which is...GIGGLE: a search engine for large-scale integrated genome analysis
By Jit 2507 days agogithub.com - GIGGLE is a genomics search engine that identifies and ranks the 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 is...MUMmer4: A fast and versatile genome alignment system
By Jit 2483 days agomummer4.github.io - MUMmer4, a substantially improved version of MUMmer that addresses genome size constraints by changing the 32-bit suffix tree data structure at the core of MUMmer to a 48-bit suffix array, and that offers improved speed through parallel processing...G-compass: a comparative genome browser
By Jit 2415 days agowww.h-invitational.jp - G-compass (http://www.h-invitational.jp/g-compass/) is a comparative genome browser. It visualizes evolutionarily conserved genomic regions between human and other 12 vertebrates based on original genome alignments pursuing higher coverage (1,2)....Circlator: automated circularization of genome assemblies using long sequencing reads
By Poonam Mahapatra 2382 days agosanger-pathogens.github.io - A tool to circularize genome assemblies. The algorithm and benchmarks are described in the Genome Biology manuscript. Citation: "Circlator: automated circularization of genome assemblies using long sequencing reads", Hunt et al, Genome Biology...
