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-based phasing or haplotype assembly. It is especially suitable for long reads, but works also well with...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 HTM...nparalleled speed. Scales easily to multi-gigabase genomes and deep-coverage sequencing. Quickly open and view data...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 feasible to study e...cifically designed for performing transcriptome assembly from high-throughput sequencing data, they are very memory-in...2187 days ago
2187 days ago
transrate: Understanding your transcriptome assembly
Transrate is software for de-novo transcriptome assembly quality analysis....your assembly in detail and compares it to experimental evidence such as the sequencing reads, reporting quality scor...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...1483 days ago
Nanopolis: polish a genome assembly
Software package for signal-level analysis of Oxford Nanopore sequencing data. Nanopolish can calculate an improved consensus sequence for a draft genome assembly, detect base modifications, call SNPs...2164 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