BEAP: Blast Extension and Assembly Program
The Blast Extension and Assembly Program (BEAP) is a computer program that uses a short starting DNA fragment, often a EST or partial gene segment, as "primer", to recursively blast nucleotide da...2160 days ago
MECAT: fast mapping, error correction, and de novo assembly for single-molecule sequencing reads
MECAT is an ultra-fast Mapping, Error Correction and de novo Assembly Tools for sin...for effectively de novo assemblying large genomes. For example, on a 32-thread computer with 2.0 GHz CPU , MECAT take...2191 days ago
LAMSA: fast split read alignment with long approximate matches
LAMSA (Long Approximate Matches-based Split Aligner) is a novel split alignment approach with faster speed and good ability of handling SV events...the-art long read aligners; mean-while, it also has good abi...2187 days ago
2187 days ago
DUPCAR: Reconstructing Contiguous Ancestral Regions with Duplications
we propose a heuristic algorithm, called DUPCAR, for reconstructing ancestral genom...rs by connecting genes into contiguous regions based on predicted adjacencies. Computer simulation was used to valida...2181 days ago
SOAP2 : Short Oligonucleotide Analysis Package 2
SOAPaligner/soap2 is a member of the SOAP (Short Oligonucleotide Analysis Package)....(2way-BWT) are developed by the algorithms research group of the Department of Computer Science, the University of Ho...2179 days ago
AfterQC: Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data AfterQC can simply go through all fastq files in a folder and then output three folders: good, bad and QC folders, which contains good rea...2142 days ago
JBrowse: Embeddable genome browser built completely with JavaScript and HTML5
JBrowse is a fast, embeddable genome browser built completely with JavaScript and H...enomes and deep-coverage sequencing. Quickly open and view data files on your computer without uploading them to any...2142 days ago
Snippy: Rapid haploid variant calling and core SNP phylogeny
Snippy finds SNPs between a haploid reference genome and your NGS sequence reads. I...ns/deletions (indels). It will use as many CPUs as you can give it on a single computer (tested to 64 cores). It is d...2030 days ago
FinisherSC:a repeat-aware tool for upgrading de novo assembly using long reads
Here is the command to run the tool: python finisherSC.py destinedFolder mummerPath If you are running on server computer and would like to use multipl...2090 days ago