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DIAL
By Abhimanyu Singh 3543 days agowww.bx.psu.edu - A computational pipeline for identifying single-base substitutions between two closely related genomes without the help of a reference genome. DIAL works even when the depth of coverage is insufficient for de novo assembly, and it can be extended to...MyCC: Accurate binning of metagenomic contigs via automated clustering sequences using information...
By Jit 3541 days agosourceforge.net - MyCC, an automated binning tool that combines genomic signatures, marker genes and optional contig coverages within one or multiple samples, in order to visualize the metagenomes and to identify the reconstructed genomic fragments. More...MaxBin: software for binning assembled metagenomic sequences based on an Expectation-Maximization...
By Jit 3538 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 3537 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:...Software and Tools to detect structure variation with long reads !!
By Archana Malhotra 3529 days agoStructural variation caller tools using long readsBacterial genome assembly !!
By Jit 3478 days agobioinformatics.uconn.edu - This tutorial will serve as an example of how to use free and open-source genome assembly and secondary scaffolding tools to generate high quality assemblies of bacterial sequence data. The bacterial sample used in this tutorial will be...NCBI Prokaryotic Genome Annotation Pipeline
By Jit 3467 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 3292 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...funannotate: Eukaryotic Genome Annotation Pipeline
By Jit 2976 days agogithub.com - Funannotate is a genome prediction, annotation, and comparison software package. It was originally written to annotate fungal genomes (small eukaryotes ~ 30 Mb genomes), but has evolved over time to accomodate larger genomes. The impetus for this...Earth BioGenome Project
By Jit 3123 days agoThe central goal of the Earth BioGenome Project is to understand the evolution and organization of life on our planet by sequencing and functionally annotating the genomes of 1.5 million known species of eukaryotes
