Jit
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HISAT2: a fast and sensitive alignment program for mapping next-generation sequencing reads
By Rahul Nayak 3012 days agogithub.com - HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome). Based on an extension of BWT for...Cactus: a reference-free whole-genome multiple alignment program
By Jit 2551 days agogithub.com - Cactus is a reference-free whole-genome multiple alignment program. The principal algorithms are described here: https://doi.org/10.1101/gr.123356.111 Cactus uses substantial resources. For primate-sized genomes (3 gigabases each), you should...shovill: Assemble bacterial isolate genomes from Illumina paired-end reads
By BioStar 2042 days agogithub.com - Shovill is a pipeline which uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take...Genomicus: genome browser that enables users to navigate in genomes in several dimensions
By Jit 1620 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...Bactopia: a flexible pipeline for complete analysis of bacterial genomes
By Abhi 789 days agobactopia.github.io - Bactopia is a flexible pipeline for complete analysis of bacterial genomes. The goal of Bactopia is process your data with a broad set of tools, so that you can get to the fun part of analyses quicker! Bactopia was inspired by Staphopia, a...Multi-CAR: a tool of contig scaffolding using multiple references
By Rahul Nayak 3075 days agogenome.cs.nthu.edu.tw - we design a simple heuristic method to further revise our single reference-based scaffolding tool CAR into a new one called Multi-CAR such that it can utilize multiple complete genomes of related organisms as references to more accurately order and...FGENESH - Program for predicting multiple genes in genomic DNA sequences
By BioStar 2786 days agowww.softberry.com - FGENESH is the fastest (50-100 times faster than GenScan) and most accurate gene finder available - see the figure and the table below. In recent rice genome sequencing projects, it was cited "the most successful (gene finding) program (Yu et...Termal: a fast and interactive terminal-based viewer for multiple sequence alignments
By LEGE 318 days agogithub.com - termal, a fast, interactive, terminal-based viewer for multiple sequence alignments (MSAs), designed for use on remote systems such as high-performance computing (HPC)...COPE: an accurate k-mer-based pair-end reads connection tool to facilitate genome assembly
By Jit 3165 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...Reference-free prediction of rearrangement breakpoint reads
By Neel 3073 days agocode.google.com - lideSort-BPR ( b reak p oint r eads) is based on a fast algorithm for all-against-all comparisons of short reads and theoretical analyses of the number of neighboring reads. When applied to a dataset with a sequencing...
