Dahak: benchmarking and containerization of tools for analysis of complex non-clinical metagenomes.
Dahak is a software suite that integrates state-of-the-art open source tools for metagenomic analyse...tagenomic analysis workflows including data pre-processing, metagenome assembly, taxonomic and functional classification, genome...1551 days ago
CSAR-web: a web server of contig scaffolding using algebraic rearrangements
CSAR-web is a web-based tool that allows the users to efficiently and accuratel...and orient) the contigs of a target draft genome based on a complete or incomplete reference genome from a related organism. ...iently and accurately scaffold their draft genomes...1550 days ago
RefKA: A fast and efficient long-read genome assembly approach for large and complex genomes
RefKA, a reference-based approach for long read genome assembly. This approach relies on breaking up a closely related reference genome into bins, aligning k-mers unique to each bin with PacBio reads, and then assembling each bin in parallel followed by a final bin-stitching step.1529 days ago
HASLR: a hybrid assembler which uses both second and third generation sequencing reads
HASLR, a hybrid assembler which uses both second and third generation sequencing reads to efficiently generate accurate genome...1526 days ago
NucDiff: In-depth characterization and annotation of differences between two sets of DNA sequences
NucDiff locates and categorizes differences between two closely related nucleotide sequences. It is able to deal with very fragmented genomes, structural rearrangements a...mblies with each other or with available reference genomes...1525 days ago
Synteny and Rearrangement Identifier (SyRI)
SyRI is a comprehensive tool for predicting genomic differences between related genomes using whole-genome assemblies (WGA). The assemblies are aligned using whole-genome alignment tools, and these align...1525 days ago
LR_Gapcloser: a tiling path-based gap closer that uses long reads to complete genome assembly
LR_Gapcloser is a gap closing tool using long reads from studied species. The long reads could be downloaed from public read archive database (for instance, NCBI SRA da...1516 days ago
GRIDSS: the Genomic Rearrangement IDentification Software Suite
GRIDSS is a module software suite containing tools useful for the detection of genomic rearrangements. GRIDSS includes a genome-wide break-end assembler, as...sed on alignment-guided positional de Bruijn graph genome-...1513 days ago
Genobuntu: Package for Next Generation Sequencing and Genome Assembly
Genobuntu is a software package containing more than 70 software and packages oriente...nt version, Genobuntu supports pre assembly tools, genome assemblers as well as post as...r both novices and experts working in the field of genome...1512 days ago
Mercator: Multiple Whole-Genome Orthology Map Construction
Whole-genome homology maps attempt to identify the evolutionary re...s between and within multiple genomes. The term "syntenic" is ofte...describe regions of multiple genomes that are believed to have ev...us" instead. Ideally, given K genomes, we would like to identify a...1511 days ago