MIX: Combining multiple assemblies from NGS data
Mix is a tool that combines two or more draft assemblies, without relying on a reference genome and has the goal to reduce contig fragmentation and thus speed-up genome finishing. The proposed algor...2246 days ago
kWIP: The k-mer weighted inner product, a de novo estimator of genetic similarity
The k-mer Weighted Inner Product. This software implements a de novo, alignment fre...e to calculate the genetic dissimilarity between samples without any reference genome, and without assembling one....2225 days ago
SEX-DETector: A Probabilistic Approach to Study Sex Chromosomes in Non-Model Organisms
SEX-DETector is a probabilistic method that relies on RNAseq data from a cross (pare...-DETector work? SEX-DETector does not require prior sequencing of a reference genome: the same sequencing data can...2223 days ago
CrossMap: a program for convenient conversion of genome coordinates
CrossMap is a program for convenient conversion of genome coordinates (or annotation files) between..., VCF. CrossMap is designed to liftover genome coordinates between assemblie...rogram for aligning sequences to reference genome. We do not recommend using...2223 days ago
2223 days ago
Ranbow: a haplotype assembler for polyploid genomes
Ranbow is a haplotype assembler for polyploid genomes. It has been developed for the haplotype assembly of the hexaploid sweet potato genome, which is highly heterozygous...nbow can also be applied to other polyploid genomes. After a first phasing, Ranb...2222 days ago
“One code to find them all”: a perl tool to conveniently parse RepeatMasker output files
One code to find them all is a set of perl scripts to extract useful information fro...sta files Compute summary statistics for each TE family (number of TE copies, genome coverage...) Ambiguous cases...2219 days ago
EAGLER: a scaffolding tool for long reads.
EAGLER is a scaffolding tool for long reads. The scaffolder takes as input a draft genome created by any NGS assembler...2219 days ago
HALC: High throughput algorithm for long read error correction
HALC, a high throughput algorithm for long read error correction. HALC aligns the lo...g read region can be aligned to at least one contig region, including its true genome region’s repeats in the conti...2215 days ago
PRICE (Paired-Read Iterative Contig Extension), a de novo genome assembler implemented in C++.
We are pleased to release PRICE (Paired-Read Iterative Contig Extension), a de novo genome assembler implemented in C++....name describes the strategy that it implements for genome assembly: PRICE uses paired-r...2212 days ago