HISAT2: a fast and sensitive alignment program for mapping next-generation sequencing reads
HISAT2 is a fast and sensitive alignment program for mapping next-generatio...(both DNA and RNA) to a population of human genomes (as well as to a single reference genome). Based on an extension of BW...index that represents a population of human genomes...2247 days ago
EvidentialGene: tr2aacds, mRNA Transcript Assembly Software
EvidentialGene is a genome informatics project, "Evidence Directed Gene Constr...ecent gene assembly (de-novo and genome-assisted) methods. The basic...genes, from expressed sequences, genome assembly sequences, related sp...lGene is publicly available. See project wiki/blog for notes. Downloa...2247 days ago
Metassembler: merging and optimizing de novo genome assemblies
Metassembler combines multiple whole genome de novo assemblies into a combined c...est segments of the individual assemblies. Genome assembly projects typically run multiple algo...orithm that merges multiple assemblies of a genome into a single superior sequenc...2247 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...2247 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 dis...e to calculate the genetic dissimilarity between samples without any reference genome,...2226 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) to...-DETector work? SEX-DETector does not require prior sequencing of a reference genome:...2225 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....2224 days ago
2224 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...2223 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 transposab...sta files Compute summary statistics for each TE family (number of TE copies, genome...2220 days ago