Porechop: tool for finding and removing adapters from Oxford Nanopore reads
Porechop is a tool for finding and removing adapters from Oxford Nanopore reads. Adap...orechop performs thorough alignments to effectively find adapters, even at low sequence identity. Porechop also supp...2231 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,...2231 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:...2230 days ago
CrossMap: a program for convenient conversion of genome coordinates
...is a program for convenient conversion of genome coordinates (or annotation fi...VCF. CrossMap is designed to liftover genome coordinates between assemblies. It’s not a program for aligning sequences to reference genome. We do not recommend using C...2229 days ago
2229 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....2228 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.2227 days ago
“One code to find them all”: a perl tool to conveniently parse RepeatMasker output files
...r about transposable elements, retrieve their sequences and get some quantitative...TR-retrotransposon Retrieve corresponding TE sequences, and flanking sequences, fro...tics for each TE family (number of TE copies, genome coverage...) Ambiguous cases s...2225 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 prese...2225 days ago
2224 days ago