Jit
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Carefully opt for human reference genome
By biogeek 1770 days agolh3.github.io - Heng Li posted several issues with the human reference genomes given in these resources and suggests the following compressed FASTA file to be used as hg38/GRCh38 human reference genome. if you map reads to GRCh38 or hg38, use the...JBrowse: Embeddable genome browser built completely with JavaScript and HTML5
By Jit 2369 days agogithub.com - JBrowse is a fast, embeddable genome browser built completely with JavaScript and HTML5, with optional run-once data formatting tools written in Perl. Headline Features: Fast, smooth scrolling and zooming. Explore your genome with unparalleled...deepTools
By Martin Jones 3697 days agoUser-friendly tools for the normalization and visualization of deep-sequencing dataDIAL
By Abhimanyu Singh 2854 days agowww.bx.psu.edu - A computational pipeline for identifying single-base substitutions between two closely related genomes without the help of a reference genome. DIAL works even when the depth of coverage is insufficient for de novo assembly, and it can be extended to...mrFAST: Micro Read Fast Alignment Search Tool
By Neel 3163 days agomrfast.sourceforge.net - mrFAST is a read mapper that is designed to map short reads to reference genome with a special emphasis on the discovery of structural variation and segmental duplications. mrFAST maps short reads with respect to user defined error threshold,...sockeye
By Jit 2866 days agowww.bcgsc.ca - This sockeye software uses the Ensembl database project to import sequence and annotation information from several eukaryotic species. A user can additionally import their own custom sequence and annotation data. Individual annotation objects...MetaGraph: Ultra Scalable Framework for DNA Search, Alignment, Assembly
By Abhi 197 days agometagraph.ethz.ch - The MetaGraph framework is designed to work with a wide range of input data sets, indexing from a few samples up to the contents of entire archives with hundreds of thousands of records. The indexing workflow always follows the same principle,...MUMmer4: A fast and versatile genome alignment system
By Jit 2515 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...Mulan: Multiple-sequence local alignment and visualization for studying function and evolution
By Jit 2313 days agowww.ncbi.nlm.nih.gov - Mulan: Multiple-sequence local alignment and visualization for studying function and evolution Mulan (http://mulan.dcode.org/), a novel method and a network server for comparing multiple draft and finished-quality sequences to identify functional...coursera genome assembly tutorial
By Jit 2585 days agogithub.com - Solutions to Coursera Genome Sequencing (Bioinformatics II)
