FGENESH - Program for predicting multiple genes in genomic DNA sequences
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,...rogram (Yu et al. (2002) Science 296:79) and was used to produce 87% of all high-...2019 days ago
NanoPack: visualizing and processing long-read sequencing data
The NanoPack tools are written in Python3 and released under the GNU GPL3.0 License. The source code...ster/nanopack, together with links to separate scripts and t...ntation. The scripts are compatible with Linux, Mac OS and the MS...2014 days ago
Hawkeye: an interactive visual analytics tool for genome assemblies
Genome sequencing remains an inexact science, and genome sequences can contain significant errors if t...or genome assemblies, designed to aid in identifying and c...levels of an assembly along with summary statistics and assembly metr...2007 days ago
EXCAVATOR: detecting copy number variants from whole-exome sequencing data
EXCAVATOR, for the detection of copy number variants (CNVs) from whole-exome sequencing data. EXCAVATOR combin...e EXCAVATOR on three datasets and c...well as in clinical research and diagnostics. EXCAVATOR is freely ava...iants (CNVs) from whole-exome sequencing data.EXCAVATOR has been publi...2004 days ago
kallisto: a program for quantifying abundances of transcripts from bulk and single-cell RNA-Seq data
kallisto is a program for quantifying abundances of transcripts from bulk and single-cell RNA-Seq data, or...ignment. On benchmarks with standard RNA-Seq data, kallist...using only the read sequences and a...Pimentel, Páll Melsted and Lior Pachter, Near-optimal prob...2001 days ago
2001 days ago
SvABA: Genome-wide detection of structural variants and indels by local assembly
SvABA is a method for detecting structural variants in sequencing data using genome-wide...Assembler) by Jared Simpson, and BWA-MEM by Heng Li....parsed to identify variants. Sequencing reads are then realigned to the contigs with BWA-MEM, and variants are scored by their read su...1987 days ago
1987 days ago
nQuire: A statistical framework for ploidy estimation using NGS short-read data
nQuire implements a set of commands to estimate ploidy level of individu...here recent polyploidization occurred and intraspecific ploidy variatio...ifically, nQuire uses next-generation seque...stinguish between diploids, triploids and tetraploids, on the basis of frequen...1978 days ago
MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons
MACSE aligns coding NT sequences with respect to their AA translati...s to contain multiple frameshifts and/or stop codons. MACSE is henc...ifts in public database sequences and in aligning next-generation seque...uences accounting for frameshifts and stop codons.Vincent Ranwez, Sé...1960 days ago