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 sequence similarity search tool providing significant accelerations of seeds-based heuristi...hms. Relying on unique software architecture, PLAST takes fu...teria (E-Value, identity, coverage, alignment length, etc.),...2411 days ago
dnaPipeTE: de-novo assembly & annotation Pipeline for Transposable Elements
dnaPipeTE (for de-novo assembly & annotation Pipeline for Transposable Elements), is a pip...to find, annotate and quantify Transposable Elements in small s...is very useful to quantify the proportion of TEs in newly seque...BE: http://lbbe.univ-lyon1.fr/-Equipe-Elements-transposable...2410 days ago
MinION_GC: An R script to do some QC on MinION data
Other tools focus on getting data out of the fastq or fast5 files, which is slow and computationally intensive. The benefit of this approach is that it works on a sin...mall, .txt summary file. So it's a lot quicker than most other things out th...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 taxonomi...Based on a database of given genomes, the program allows the user to ...of the NCBI taxonomy, and then to collect reads from the metagenome using...2408 days ago
Bandage: interactive visualization of de novo genome assemblies
Bandage (a Bioinformatics Application for Navigating De novo Assembly Graphs Easily) is a tool for vis...y graphs with connections. Users can zoom in to specific area...xtracting sequences. BLAST searches can be performed within t...y and implementation: Source code and binaries are freel...2408 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 normalized contact maps. Since version 2...Hi-C protocols, including digestion protocols as well as protocols t...situ Hi-C, DNase Hi-C, Micro-C, capture-C, capture Hi-C or HiChip da...2407 days ago
COPE: an accurate k-mer-based pair-end reads connection tool to facilitate genome assembly
An efficient tool called Connecting Overlapped Pair-End (COPE) reads, to connect overlapping pair-end reads using k-mer frequenc...on 30× simulated pair-end reads from Arabidopsis thaliana with 1...hed tool FLASH. When COPE is applied to real reads for genome assembly,...2407 days ago
Musket: a multistage k-mer spectrum based corrector
...well-established leading next-generation sequencing read error correction algorithm...tting Illumina sequencing. This corrector employs the k-mer...s in a multistage workflow. Our performance evaluation results, i...g a master-slave model and demonstrates superior parallel scalabi...2407 days ago
ACANA: An accurate and consistent alignment tool for DNA sequences
ACANA is an accurate and consistent alignment tool for DNA sequences. ACANA is specifically designed for aligning sequences that share only s...me moderately conserved regions and/or have a high frequency of long...ily related regions of sequences in order to achieve the best alignm...2406 days ago
2406 days ago