MIX: Combining multiple assemblies from NGS data
...t 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...2248 days ago
kWIP: The k-mer weighted inner product, a de novo estimator of genetic similarity
...ic dissimilarity which operates upon raw sequencing reads. It is able to calculate the genetic dissimilarity between samples without any reference genome, and without assembling one....2227 days ago
SEX-DETector: A Probabilistic Approach to Study Sex Chromosomes in Non-Model Organisms
...cated on the non recombining part of sex chromosomes). How does SEX-DETector work? SEX-DETector does not require prior sequencing of a reference genome: the same sequencing data can...2226 days ago
CrossMap: a program for convenient conversion of genome coordinates
...sMap is a program for convenient conversion of genome coordinates (or annotation fi.../GTF, VCF. CrossMap is designed to liftover genome coordinates between assemblie...a program for aligning sequences to reference genome. We do not recommend using...2225 days ago
2225 days ago
Ranbow: a haplotype assembler for polyploid genomes
Ranbow is a haplotype assembler for polyploid genomes. It has been developed for th...plotype assembly of the hexaploid sweet potato genome, which is highly heterozygous...Ranbow can also be applied to other polyploid genomes. After a first phasing, Ranb...2224 days ago
“One code to find them all”: a perl tool to conveniently parse RepeatMasker output files
...orresponding TE sequences, and flanking sequences, from the local fasta files Compute summary statistics for each TE family (number of TE copies, genome coverage...) Ambiguous cases...2221 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 and a set of long reads. The long reads are used to extend the c...2221 days ago
HALC: High throughput algorithm for long read error correction
...ame species with a relatively low identity requirement so that a long read region can be aligned to at least one contig region, including its true genome region’s repeats in the conti...2217 days ago
PRICE (Paired-Read Iterative Contig Extension), a de novo genome assembler implemented in C++.
...ed to release PRICE (Paired-Read Iterative Contig Extension), a de novo genome assembler implemented in C++. Its name describes the strategy that it implements for genome assembly: PRICE uses paired-r...2214 days ago