EvidentialGene: tr2aacds, mRNA Transcript Assembly Software
EvidentialGene is a genome informatics project, "Evidence Directed Gene Construction f...ction, and more recent gene assembly (de-novo and genome-assisted) methods. The basic...all evidence for genes, from expressed sequences, genome assembl...2250 days ago
Metassembler: merging and optimizing de novo genome assemblies
Metassembler combines multiple whole genome de novo assemblies into a combined consensus ass...the best segments of the individual assemblies. Genome assembly projects typically r...r algorithm that merges multiple assemblies of a genome into a...2250 days ago
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 finishi...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 d...to calculate the genetic dissimilarity between samples without any reference genome, and wi...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)...ETector work? SEX-DETector does not require prior sequencing of a reference genome: the sa...2227 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 diff.../GTF, VCF. CrossMap is designed to liftover genome coordinates between assemblie...a program for aligning sequences to reference genome. We...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. After...2226 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 transpos...a files Compute summary statistics for each TE family (number of TE copies, genome coverag...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 present...2223 days ago