Scallop: reference-based transcriptome assembler for RNA-seq
...also achieves both transcripts parsimony and coverage deviation minimization. Scallop paper has been published at Nature Biotechnology. The datasets and scripts used in this pape...2186 days ago
MCMCTREE: a phylogenetic program for Bayesian estimation of species divergence times
...dified from dataset of Inoue et al. (2010). Here we conduct a commonly used time estimation method, "Approximate Likelihood Method", for the datasets including more than 10 specie...2161 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 bacte...2158 days ago
npScarf: real-time scaffolder using SPAdes contigs and Nanopore sequencing reads
...at connect contigs from a draft genomes to generate sequences that are closer to finish. These pipelines can run on a single laptop for microbial datasets. In real-time mode, it can be...2152 days ago
MECAT: fast mapping, error correction, and de novo assembly for single-molecule sequencing reads
...ent PBcR-Mhap pipeline. MECAT performance were compared with PBcR-Mhap pipeline, FALCON and Canu(v1.3) in five real datasets. The quality of assembled con...2183 days ago
2179 days ago
LAMSA: fast split read alignment with long approximate matches
...c programming (SDP)-based split alignment approach to handle the large or non-co-linear variants. We benchmarked LAMSA with simulated and real datasets having various read lengths a...2179 days ago
JBrowse: Embeddable genome browser built completely with JavaScript and HTML5
...source requirements. In fact, JBrowse has no back-end server code, just tools for formatting data files to be read directly over HTTP. Serve huge datasets from a single low-cost cloud...2134 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 counts. The following tools are currently available in KAT: hist:...1979 days ago
Bokeh: An interactive visualization library that targets modern web browsers for presentation
...egant, concise construction of versatile graphics, and to extend this capability with high-performance interactivity over very large or streaming datasets. Bokeh can help anyone who wo...2092 days ago