Multi-CAR: a tool of contig scaffolding using multiple references
we design a simple heuristic method to further revise our single reference-based scaffol...lti-CAR such that it can utilize multiple complete genomes of related organisms as refer...enetic relationships among the draft and reference genomes...2311 days ago
Reference-free prediction of rearrangement breakpoint reads
lideSort-BPR ( b reak p oint r eads) is based on a fast algorithm for all-against-all comparisons of short reads and theoretical analyses of the number of neighboring...2309 days ago
Mesquite: A modular system for evolutionary analysis
Mesquite is modular, extendible software for evolutionary biology, designed to help b...others do non-phylogenetic multivariate analysis. Because it is modular, the analyses available depend on the modul...2304 days ago
ALPHA: A Toolkit for Automated Local Phylogenomic Analyses
Automated Local Phylogenomic Analyses, or ALPHA, is a python-based application that provides an intuitive user interface for phylogenetic analyses and data visualization. It ha...2296 days ago
NGMLR: long-read mapper designed to align PacBio or Oxford Nanopore
CoNvex Gap-cost alignMents for Long Reads (ngmlr) is a long-read mapper designed to sensitively align PacBilo or Oxford Nanopore to (large) reference genomes....2261 days ago
HISAT2: a fast and sensitive alignment program for mapping next-generation sequencing reads
HISAT2 is a fast and sensitive alignment program for mapping next-generation sequen...reads (both DNA and RNA) to a population of human genomes (as well as to a single refer...al GFM index that represents a population of human genomes,...2248 days ago
2225 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...ich is highly heterozygous. Ranbow can also be applied to other polyploid genomes....2224 days ago
Cerulean: A hybrid assembly using high throughput short and long reads
Cerulean extends contigs assembled using short read datasets like Illumina paired-end reads using long reads like PacBio RS long reads. Cerulean v0.1 has been implemented with bacterial genomes...2220 days ago
npScarf: real-time scaffolder using SPAdes contigs and Nanopore sequencing reads
...pScarf (jsa.np.npscarf) is a program that connect contigs from a draft genomes to generate sequences that ar...tasets. In real-time mode, it can be integrated with simple structural analyses such as gene ordering, plasmi...2214 days ago