Jit
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MetaBAT: An Efficient Tool for Accurately Reconstructing Single Genomes from Complex Microbial...
By Jit 2821 days agobitbucket.org - MetaBAT, An Efficient Tool for Accurately Reconstructing Single Genomes from Complex Microbial Communities Grouping large genomic fragments assembled from shotgun metagenomic sequences to deconvolute complex microbial communities, or metagenome...BRIG
By Jit 2839 days agobrig.sourceforge.net - BRIG is a free cross-platform (Windows/Mac/Unix) application that can display circular comparisons between a large number of genomes, with a focus on handling genome assembly data. The application is available...splitbam: splits a BAM by chromosomes
By Jit 2827 days agocode.google.com - splitbam splits a BAM by chromosomes. Using the reference sequence dictionary (*.dict), it also creates some empty BAM files if no sam record was found for a chromosome. A pair of 'mock' SAM-Records can also be added to those empty BAMs to...MaxBin: software for binning assembled metagenomic sequences based on an Expectation-Maximization...
By Jit 2821 days agodownloads.jbei.org - MaxBin is software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm. Users can understand the underlying bins (genomes) of the microbes in their metagenomes by simply providing assembled metagenomic...GroopM: Metagenomic binning toolset
By Jit 2820 days agogithub.com - GroopM is a metagenomic binning toolset. It leverages spatio-temoraldynamics (differential coverage) to accurately (and almost automatically)extract population genomes from multi-sample metagenomic datasets. GroopM is largely parameter-free. Use:...DBG2OLC:Efficient Assembly of Large Genomes Using Long Erroneous Reads of the Third Generation...
By Jit 2777 days ago Comments (1)github.com - DBG2OLC:Efficient Assembly of Large Genomes Using Long Erroneous Reads of the Third Generation Sequencing Technologies Our work is published in Scientific Reports: Ye, C. et al. DBG2OLC: Efficient Assembly of Large Genomes Using Long Erroneous...NCBI Prokaryotic Genome Annotation Pipeline
By Jit 2750 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...GAPPadder: A Sensitive Approach for Closing Gaps on Draft Genomes with Short Sequence Reads
By Jit 2387 days agogithub.com - This software is provided ``as is” without warranty of any kind. In no event shall the author be held responsible for any damage resulting from the use of this software. The program package, including source codes, executables, and this...GMcloser: closing gaps in assemblies accurately with a likelihood-based selection of contig or...
By Shruti Paniwala 2359 days agoacademic.oup.com - GMcloser uses likelihood-based classifiers calculated from the alignment statistics between scaffolds, contigs and paired-end reads to correctly assign contigs or long reads to gap regions of scaffolds, thereby achieving accurate and efficient gap...
