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 fi...2250 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 free measure of sample genetic di...to calculate the genetic dissimilarity between samples without any reference genome, a...2229 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 (parents and progeny of each sex) t...DETector work? SEX-DETector does not require prior sequencing of a reference genome: t...2228 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 diffe...F/GTF, VCF. CrossMap is designed to liftover genome coordinates between assemblie...t a program for aligning sequences to reference genome....2227 days ago
2227 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.... Ranbow can also be applied to other polyploid genomes....2226 days ago
GLEAN: an unsupervised learning system to integrate disparate sources of gene structure evidence
GLEAN is an unsupervised learning system to integrate disparate sources of gene structure evidence (gene model predictions, EST/protein genomic sequence alignments, SAGE/peptide tags, etc) to produce a consensus gene prediction, without prior training.2225 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 from RepeatMasker about transposa...ta files Compute summary statistics for each TE family (number of TE copies, genome co...2223 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 contigs presen...2223 days ago
HALC: High throughput algorithm for long read error correction
HALC, a high throughput algorithm for long read error correction. HALC aligns the long reads to short read contigs...read region can be aligned to at least one contig region, including its true genome re...2219 days ago