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P_RNA_scaffolder: a fast and accurate genome scaffolder using paired-end RNA-sequencing reads
By BioStar 2934 days agowww.fishbrowser.org - P_RNA_scaffolder is a novel scaffolding tool using Pair-end RNA-seq to scaffold genome fragments. The method is suitable for most genomes. The program could utilize Illumina Paired-end RNA-sequencing reads from target speciesies. Our method provides...JBrowse: Embeddable genome browser built completely with JavaScript and HTML5
By Jit 3004 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...Meraculous: De Novo Genome Assembly with Short Paired-End Reads
By Jit 3238 days agowww.ncbi.nlm.nih.gov - We describe a new algorithm, meraculous, for whole genome assembly of deep paired-end short reads, and apply it to the assembly of a dataset of paired 75-bp Illumina reads derived from the 15.4 megabase genome of the haploid yeast Pichia...COPE: an accurate k-mer-based pair-end reads connection tool to facilitate genome assembly
By Jit 3209 days agoftp.genomics.org.cn - An efficient tool called Connecting Overlapped Pair-End (COPE) reads, to connect overlapping pair-end reads using k-mer frequencies. We evaluated our tool on 30× simulated pair-end reads from Arabidopsis thaliana with 1% base error. COPE...Biological databases !
By BioStar 2411 days ago Comments (4)ftp.ncbi.nih.gov - Now a days there are a lots of genomics databases available around the world. This bookmark is created to provide all links in one place ... ftp://ftp.ncbi.nih.gov/genomes/ https://hgdownload.soe.ucsc.edu/downloads.htmlPHYMMBL
By Jit 3631 days agowww.cbcb.umd.edu - Metagenomics sequencing projects collect samples of DNA from uncharacterized environments that may contain hundreds or even thousands of species. One of the main challenges in analyzing a metagenome is phylogenetic classification of raw sequence...Maq: Mapping and Assembly with Quality
By Jit 3588 days agomaq.sourceforge.net - Maq stands for Mapping and Assembly with Quality It builds assembly by mapping short reads to reference sequences. Maq is a project hosted by SourceForge.net. The project page is available athttp://sourceforge.net/projects/maq/....PEAR
By Jit 3561 days agosco.h-its.org - PEAR is an ultrafast, memory-efficient and highly accurate pair-end read merger. It is fully parallelized and can run with as low as just a few kilobytes of memory. PEAR evaluates all possible paired-end read overlaps and without requiring the...Software and Tools to detect structure variation with long reads !!
By Archana Malhotra 3475 days agoStructural variation caller tools using long readsLACHESIS: Genome Assembly with Hi-C-based Contact Probability Maps (LACHESIS)
By Jit 3050 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...
