Jit
Enthusiast computational biologist with business dream !!!
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Multi-metagenome assembly
By Radha Agarkar 2823 days agogithub.com - This project contains scripts and tutorials on how to assemble individual microbial genomes from metagenomes, as described in: Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomesMads...PhenoGram
By Jit 2819 days ago Comments (1)ritchielab.psu.edu - With PhenoGram researchers can create chomosomal ideograms annotated with lines in color at specific base-pair locations, or colored base-pair to base-pair regions, with or without other annotation. PhenoGram allows for annotation of chromosomal...Multigenome assembly
By Jit 2813 days agogithub.com - This project contains scripts and tutorials on how to assemble individual microbial genomes from metagenomes, as described in: Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes Mads...A Post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs
By Abhimanyu Singh 2753 days agowww.sanger.ac.uk - PAGIT addresses the need for software to generate high quality draft genomes. It is based on a series of programs that we developed: ABACAS, that is able to contiguate contigs from a de novo assembly against a closely related reference. IMAGE, an...NCBI Prokaryotic Genome Annotation Pipeline
By Jit 2749 days agowww.ncbi.nlm.nih.gov - NCBI Prokaryotic Genome Annotation Pipeline is designed to annotate bacterial and archaeal genomes (chromosomes and plasmids). Genome annotation is a multi-level process that includes prediction of protein-coding genes, as well as other functional...Meraculous: De Novo Genome Assembly with Short Paired-End Reads
By Jit 2575 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...MeDuSa: a multi-draft based scaffolder
By Abhimanyu Singh 2476 days agogithub.com - MeDuSa (Multi-Draft based Scaffolder), an algorithm for genome scaffolding. MeDuSa exploits information obtained from a set of (draft or closed) genomes from related organisms to determine the correct order and orientation of the contigs. MeDuSa...Installing Bandage on Ubunty !
By Jit 2392 days agoinstructions successfully build Bandage on a fresh installation of Ubuntu 14.04Hapsembler: An Assembler for Highly Polymorphic Genomes
By Jit 2379 days agocompbio.cs.toronto.edu - Hapsembler is a haplotype-specific genome assembly toolkit that is designed for genomes that are rich in SNPs and other types of polymorphism. Hapsembler can be used to assemble reads from a variety of platforms including Illumina and Roche/454....
