Jit
Enthusiast computational biologist with business dream !!!
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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...Reference Sequence Resource!
By LEGE 1166 days agowww.encodeproject.org - The ENCODE project uses Reference Genomes from NCBI or UCSC to provide a consistent framework for mapping high-throughput sequencing data. In general, ENCODE data are mapped consistently to 2 human (GRCH38, hg19) and 2 mouse...DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication
By Jit 2567 days agohttps://dfast.nig.ac.jp/ - We developed a prokaryotic genome annotation pipeline, DFAST, that also supports genome submission to public sequence databases. DFAST was originally started as an on-line annotation server, and to date, over 7,000 jobs have been processed since its...Circlator: automated circularization of genome assemblies using long sequencing reads
By Poonam Mahapatra 2385 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...mScaffolder: A comparative genome scaffolding tool
By Jit 2354 days agogithub.com - A comparative genome scaffolding tool based on MUMmer mScaffolder scaffolds a genome using an existing high quality genome as the reference. It aligns the two genomes using nucmer utility from MUMmer and then orders and orients the contigs of the...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...Simons Genome Diversity Project
By Jit 1296 days agowww.simonsfoundation.org - Complete genome sequences from more than one hundred diverse human populations All genomes in the dataset were sequenced to at least 30x coverage using Illumina technology. The sequencing reads were mapped and genotyped using a customized procedure...Project Associate-I | Project Associate-II | Senior Project Associate @ IGIB
Experience in Next Generation Sequencing (NGS) application and interest in Genomics/ Clinical / Translational Applications. OR Good computational programming skills and deep interest in working on interface of Genomics and Clinical application....BlasR Mapping single molecule sequencing reads using Basic Local Alignment with Successive...
By Jit 2377 days agobix.ucsd.edu - BLASR (Basic Local Alignment with Successive Refinement) for mapping Single Molecule Sequencing (SMS) reads that are thousands to tens of thousands of bases long with divergence between the read and genome dominated by insertion and deletion...
