Ranbow: a haplotype assembler for polyploid genomes
Ranbow is a haplotype assembler for polyploid genomes. It has been developed for th...g, Ranbow utilizes the assembled haplotypes to improve the accuracy of variant calling results and to infer the evol...2181 days ago
KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies
KAT is a suite of tools that analyse jellyfish hashes or sequence files (fasta or fastq) using kmer counts. The f...in the K-mer spectra in order to determine how much content is present in each peak....1997 days ago
NextSV: a meta-caller for structural variants from low-coverage long-read sequencing data
NextSV, a meta SV caller and a computational pipeline to perform SV calling from low coverage long-read sequencing d...2114 days ago
PureCN: copy number calling and SNV classification using targeted short read sequencing
This package estimates tumor purity, copy number, and loss of heterozygosity (LOH),...A, Yu K, Campbell C, Chiang D, Morrissey M (2016). “PureCN: Copy number calling and SNV classification using...2112 days ago
Snippy: Rapid haploid variant calling and core SNP phylogeny
Snippy finds SNPs between a haploid reference genome and your NGS sequence reads. It will find both substitutions (snps) and insertions/deletions (indels). It will use...2041 days ago
Rainbow: an integrated tool for efficient clustering and assembling RAD-seq reads
Rainbow is developed to provide an ultra-fast and memory-efficient solution to clus...ters reads using a spaced seed method. Then, Rainbow implements a heterozygote calling like strategy to divide poten...2041 days ago
1981 days ago
EXCAVATOR: detecting copy number variants from whole-exome sequencing data
EXCAVATOR, for the detection of copy number variants (CNVs) from whole-exome sequen...ation procedure with a novel heterogeneous hidden Markov model algorithm and a calling method that classifies genomi...1964 days ago
RaGOO: Fast Reference-Guided Scaffolding of Genome Assembly Contigs
Alonge M, Soyk S, Ramakrishnan S, Wang X, Goodwin S, Sed...s less than a minute and the whole pipeline with SV calling takes ~2 minutes. Intact ord...ontig correction GFF lift-over Structural variant calling with and integrated version o...1860 days ago
multiPhATE: bioinformatics pipeline for functional annotation of phage isolates
multiple-genome Phage Annotation Toolkit and Evaluator (multiPhATE). multiPhATE is...ed set of phage genomes. This tool incorporates a de novo phage gene-calling algorithm and assigns putativ...1832 days ago