Scallop: reference-based transcriptome assembler for RNA-seq
Scallop is an accurate reference-based transcript assembler. Scallop features its high accuracy in assembling multi-exon transcripts as well as lowly expressed transcripts. Scallop...2209 days ago
HISAT2: a fast and sensitive alignment program for mapping next-generation sequencing reads
...itive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome). Based on an extensio...2209 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 finishing. The...2209 days ago
kWIP: The k-mer weighted inner product, a de novo estimator of genetic similarity
...le genetic dissimilarity which operates upon raw sequencing reads. It is able to calculate the genetic dissimilarity between samples without any reference genome, and without assemblin...2188 days ago
SEX-DETector: A Probabilistic Approach to Study Sex Chromosomes in Non-Model Organisms
...genes located 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 d...2187 days ago
CrossMap: a program for convenient conversion of genome coordinates
..., BED, GFF/GTF, VCF. CrossMap is designed to liftover genome coordinates between assemblies. It’s not a program for aligning sequences to reference genome. We do not recommen...2186 days ago
BEAP: Blast Extension and Assembly Program
...ge disequilibrium analysis. The confidence of assembling the resulting sequences is achieved by using a known genome, such as human genome, as a reference. https://www.animalgenome...2175 days ago
RestrictionDigest: A powerful Perl module for simulating genomic restriction digests
RestrictionDigest can simulate the reference genome digestion and generate comprehensive information of the simulation. It can simulate single-enzyme digestion, double-enzyme digestion...2174 days ago
2172 days ago
GAPPadder: A Sensitive Approach for Closing Gaps on Draft Genomes with Short Sequence Reads
...e codes, executables, and this documentation, is distributed free of charge. If you use this program in a publication, please cite the following reference:Chong Chu, Xin Li, and Yufeng...2203 days ago