bpRNA: large-scale automated annotation and analysis of RNA secondary structure
bpRNA, a novel annotation tool capable of parsing RNA structures, including complex pseudoknot-containing RNAs, to yield an objective, precise, compact, unambiguous, easily-interpr...2202 days ago
2201 days ago
minialign: fast and accurate alignment tool for PacBio and Nanopore long reads
Minialign is a little bit fast and moderately accurate nucleotide sequence alignment tool designed for PacBio and Nanopore long reads. It is built on three key algorithms, minimizer-based index of the minimap overlapper, array-based seed chaining, and SIMD-parallel Smith-Waterman-Gotoh extension.2200 days ago
GenomeMapper: Simultaneous alignment of short reads against multiple genomes
GenomeMapper is a short read mapping tool designed for accurate read alignments. It quickly aligns millions of reads either with ungapped or gapped alignments. It can be used to alig...2199 days ago
SALSA: A tool to scaffold long read assemblies with Hi-C
...cd SALSA make To run the code, you will need Python 2.7, BOOST libraries and Networkx(version lower than 1.2). If you consider using this tool, please cite our publication...2179 days ago
mScaffolder: A comparative genome scaffolding tool
A comparative genome scaffolding tool based on MUMmer mScaffolder scaffolds a genome using an existing high quality genome as the reference. It aligns the two genomes using nucmer u...2179 days ago
AfterQC: Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
...other Illumina 1.8 or newer formats The author has reimplemented this tool in C++ with multithreading support to make it much faster. The new tool is called fastp and can be fo...2165 days ago
2161 days ago
KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies
...ng kmer counts. The following tools are currently available in K...ount. comp: K-mer comparison tool. Creates a matrix of shared K...y.SEquence Coverage estimator Tool. filter: Filtering tools. Co...tput coverage from the "sect" tool spectra-cn: Creates a stacke...2009 days ago
ASAR: Advanced metagenomic Sequence Analysis in R
An interactive data analysis tool for selection, aggregation and visualization of metagenomic data is presented. Functional analysis with a SEED hierarchy and pathway diagram based...2155 days ago