2223 days ago
WhatsHap: fast and accurate read-based phasing
WhatsHap is a software for phasing genomic variants using DNA sequencing reads, also called read-ba...artin et al., WhatsHap: fast and accurate read-based phasing)...Illumina, PacBio, Oxford Nanopore and o...s easy to use: Pass in a VCF and one or more BAM files, get out a pha...2223 days ago
SWALO: Scaffolding with assembly likelihood optimization
SWALO (scaffolding with assembly likelihood optimization) is a method for scaffolding based on likelihood of genome assemblies computed using generative models for sequencing. Please email your questions, comments, suggestions, and bug reports to atif.bd@gmail.com.2201 days ago
JBrowse: Embeddable genome browser built completely with JavaScript and HTML5
JBrowse is a fast, embeddable genome browser built completely with JavaScript and HTML5, with optional run-once...ures: Fast, smooth scrolling and zooming. Explore your genome...ily to multi-gigabase genomes and deep-coverage seque...large installations with thousands of tracks. Very light server resou...2191 days ago
ASplice: a scalable and memory-efficient algorithm for de novo transcriptome assembly
With increased availability of de novo assembly algorithms, it is feasi...riptome assembly from high-throughput sequencing data, they are very me...covers alternatively spliced isoforms and e...ones CD, Tarone AM. (2017) A scalable and memory-efficient algorithm for de no...2188 days ago
2188 days ago
transrate: Understanding your transcriptome assembly
Transrate is software for de-novo transcriptome assembly quality a...lysis. It examines your assembly in detail and compares it to experimental evidence such as the seque...eads, reporting quality scores for contigs and assemblies. This allows you to choos...2177 days ago
Merqury: reference-free quality and phasing assessment for genome assemblies
Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual. The k-mer spectrum of this read set can be used for independently evaluating assemb...1484 days ago
Nanopolis: polish a genome assembly
Software package for signal-level analysis of Oxford Nanopore sequencing data. Nanopolish can calculate an impr...ssembly, detect base modifications, call SNPs and indels with respect to a reference genome and more (see Nanopolish modules, below)...2165 days ago
nanofilt: Filtering and trimming of long read sequencing data
Filtering on quality and/or read length, and optional trimming after passing filters.Reads from stdin, writes to stdout. Intended to be used: directly after fastq extraction prior to mapping in a stream between extraction and mapping https://github.com/wdecoster/nanofilt2160 days ago