“One code to find them all”: a perl tool to conveniently parse RepeatMasker output files
One code to find them all is a set of perl scripts to extract useful information fr...trieve corresponding TE sequences, and flanking sequences, from the local fasta files Compute summary statistics f...2180 days ago
fragScaff: Genome Assembly with Contiguity Preserving Transposition
Contiguity preserving transposition and sequencing (CPT-seq) is an entirely in vitr...cluding source code, is available at:https://sourceforge.net/projects/fragscaff/files. Manuscript describing fragS...2201 days ago
TULIP - The Uncorrected Long read Integration Pipeline
TULIP currently consists of two Perl scripts, tulipseed.perl and tulipbulb.perl. Th...or implementations are likely to follow. Tulipseed takes as input alignments files of long reads to sparse short...2200 days ago
WhatsHap: fast and accurate read-based phasing
WhatsHap is a software for phasing genomic variants using DNA sequencing reads, als...nbsp;easy to install It is easy to use: Pass in a VCF and one or more BAM files, get out a phased VCF. Suppor...2187 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 t...2155 days ago
JBrowse: Embeddable genome browser built completely with JavaScript and HTML5
.... Quickly open and view data files on your computer without up...o any server. Supports GFF3, BED, FASTA, Wiggle, BigWig, BAM,...ex), REST, and more. BAM, BigBed, BigWig, and VCF data are displ...unks of the compressed binary files, no conversion needed. Inclu...2155 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 c...K-mers between two (or three) sequence files or hashes. sect: SEquence Co...for filtering k-mer hashes and FastQ/A files: kmer: Produces a k-mer ha...2000 days ago
2117 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 sequencin...) for different analysis purpose. The output of NextSV is in ANNOVAR-compatible bed f...2117 days ago
2116 days ago