Jit
Enthusiast computational biologist with business dream !!!
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ANItools web: a web tool for fast genome comparison within multiple bacterial strains
By Jit 2202 days agohttp://ani.mypathogen.cn/ - ANItools is a software package written by PERL scripts that can be run in a Linux/Unix system. If you want to compare bacterial genomes and calculate their average nucleotide identity (ANI), you could download and run this program directly. Or you...Sequence Ontology Bioinformatics Analysis (SOBA) tool to provide a simple statistical and graphical...
By BioStar 1586 days agowww.sequenceontology.org - We have developed the Sequence Ontology Bioinformatics Analysis (SOBA) tool to provide a simple statistical and graphical summary of an annotated genome. We envisage its use during annotation jamborees, genome comparison and for use by developers...odgi: optimized dynamic genome/graph implementation
By Abhimanyu Singh 1027 days agogithub.com - odgi provides an efficient and succinct dynamic DNA sequence graph model, as well as a host of algorithms that allow the use of such graphs in bioinformatic analyses. Careful encoding of graph entities allows odgi to efficiently...Genomicus: genome browser that enables users to navigate in genomes in several dimensions
By Jit 1000 days agowww.genomicus.bio.ens.psl.eu - Genomicus is a genome browser that enables users to navigate in genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time. Once a query gene has been entered, it...gbtools: Interactive Visualization of Metagenome Bins in R
By Jit 2800 days agojournal.frontiersin.org - We have developed gbtools, a software package that allows users to visualize metagenomic assemblies by plotting coverage (sequencing depth) and GC values of contigs, and also to annotate the plots with taxonomic information. Different sets of...fragScaff: Genome Assembly with Contiguity Preserving Transposition
By Jit 2386 days agosourceforge.net - Contiguity preserving transposition and sequencing (CPT-seq) is an entirely in vitro means of generating libraries comprised of 9216 indexed pools, each of which contains thousands of sparsely sequenced long fragments ranging from 5 kilobases to...COPE: an accurate k-mer-based pair-end reads connection tool to facilitate genome assembly
By Jit 2546 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...Hawkeye: an interactive visual analytics tool for genome assemblies
By Abhimanyu Singh 2154 days agoamos.sourceforge.net - Genome sequencing remains an inexact science, and genome sequences can contain significant errors if they are not carefully examined. Hawkeye is our new visual analytics tool for genome assemblies, designed to aid in identifying and correcting...HASLR: a tool for rapid genome assembly of long sequencing reads
By LEGE 1759 days agogithub.com - HASLR is a tool for rapid genome assembly of long sequencing reads. HASLR is a hybrid tool which means it requires long reads generated by Third Generation Sequencing technologies (such as PacBio or Oxford Nanopore) together with Next Generation...VCF Compare !
By Rahul Nayak 1040 days agowiki.bits.vib.be - compare two BWA mapping methods with the online hg18-mapped data We first operate a rapid inspection of the different BAM files using samtools flagstat. Illumina provided chr21 read mapping obtained with their GA IIx deep...
