phyloXML: XML for evolutionary biology and comparative genomics
...sed features, such as taxonomic information, gene names and identifiers, branch lengths, support values, a...n and speciation events. Using these standardized elements allows interoperability between various applica...2412 days ago
PLAST: A fast, accurate and NGS scalable bank-to-bank sequence similarity search tool
PLAST is a fast, accurate and NGS scalable bank-to-bank sequ...rch tool providing significant accelerations of seeds-based heuristic...re devices. PLAST stands for Parallel Local Sequence Alignment...lity results, Contains a fully integrated data filtering engine capa...2411 days ago
dnaPipeTE: de-novo assembly & annotation Pipeline for Transposable Elements
...de-novo assembly & annotation Pipeline for Transposable Elements), is a pipeline designed to find, annotate and quantify Transposable Elements in small sa...nbsp;http://lbbe.univ-lyon1.fr/-Equipe-Elements-transposables-.html?lang=en...2409 days ago
MetaSim A Sequencing Simulator for Genomics and Metagenomics.
Our software can be used to generate collections of synthetic reads that reflect the diverse tax...pical metagenome data sets. Based on a database of given genomes, the program allows the user to desi...2408 days ago
Bandage: interactive visualization of de novo genome assemblies
...Application for Navigating De novo Assembly Graphs Easily) is a tool for visualizing assembly graphs with connections. Users ca...th it by moving nodes, adding labels, changing colors and extracting sequences. BLAST searche...2407 days ago
HiC-Pro: an optimized and flexible pipeline for Hi-C data processing
HiC-Pro was designed to process Hi-C data, from raw fastq files (paired-end Illumina data) to the normaliz...protocols that do not require restriction enzyme such as DNase Hi-C. In practice, HiC-Pro can be used to...2406 days ago
COPE: an accurate k-mer-based pair-end reads connection tool to facilitate genome assembly
...encies. We evaluated our tool on 30× simulated pair-end reads from Arabidopsis thaliana with 1% base error. COPE connected over 99% of reads with 98.8% accuracy, which is, respectively, 10...2406 days ago
Musket: a multistage k-mer spectrum based corrector
...sket is a well-established leading next-generation sequencing read error cor...i-threaded using a master-slave model and demonstrates superior parallel scalabil...ed correctors as well as a highly competitive overall execution time.2406 days ago
ACANA: An accurate and consistent alignment tool for DNA sequences
ACANA is an accurate and consistent alignment tool for DNA sequences....ed for aligning sequences that share only some moderately conserved regions and/or...is also robust to the small changes of alignment parameters, particularly the gap e...2405 days ago
2405 days ago