The annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2020) is held online July 13-16 and the BTL group will be there, presenting several new bioinformatics technologies developed by our lab and including Meta-NanoSim, ntJoin, Physlr, RNA-Scoop and RResolver.
This is our second publication on the NanoSim tool, describing a functionality to simulate nanopore reads for transcriptome sequencing experiments. Trans-NanoSim was published in GigaScience and is an integral part of the NanoSim project, freely available from GitHub.
Our study describing the genome sequencing of the Sitka spruce mitochondrial genome was accepted for publication in Genome Biology and Evolution. In the manuscript we present the complete 5.5 Mb genome, one of the largest mitochondrial genome of a gymnosperm, assembled from Oxford Nanopore long reads and describe its complex physical structure.
Our manuscript describing ntJoin, a fast and lightweight reference-guided scaffolder, was published in Bioinformatics. Instead of alignments, ntJoin uses a mapping approach based on a graph data structure generated from ordered minimizer sketches. ntJoin can be used in a variety of different research applications, including improving a draft assembly with a reference-grade genome, a short-read assembly with a draft...
Our study describing FusionBloom, a utility for detecting transcript fusions with utility in cancer diagnostics, was just published in the peer-reviewed journal Bioinformatics.
Two studies reporting on the complete chloroplast genomes and gene annotations of white and Engelmann spruce are now published in the peer-reviewed journal Microbiology Resource Announcements.
Our study describing ntEdit, a fast and scalable technology to polish and ‘haploidize’ genome sequences, was just published in the peer-reviewed journal Bioinformatics.
We introduce ORCA, a Docker image with hundreds of bioinformatics tools/dependencies, simplifying software installs. ORCA was recently published in the peer-reviewed journal Bioinformatics.
Our latest work on antimicrobial peptide (AMP) discovery in bullfrogs was just published in the peer-reviewed journal Scientific Reports The paper describes the AMP discovery bioinformatics pipeline and functional assays to test their efficacy against microbes.
Our study presenting Tigmint, a bioinformatics utility to detect and correct errors in genome assemblies using linked reads is published in the peer-reviewed journal BMC Bioinformatics.
Our latest genome assembly scaffolder, ARKS, was just published in the peer-reviewed journal BMC bioinformatics The paper describes a new read alignment-free methodology that employs kmer-based read mapping and improves assembly runtime. In the paper we present benchmarks on human genome draft assemblies and show how linked reads can improve drafts assembled with the same sequencing data further.
The Research Programmer: •Develops and implements new algorithms •Works with the BTL’s large C/C++ code base (improve existing modules, create new ones, etc.) •Works on complex biological problems in which analysis of sequence data requires in-depth evaluation More info available here
RECOMB 2018 will be taking place in Paris, France, from April 21-24th. RECOMB-Seq is one of its four satellite workshops this year, taking place from April 19-20th, bringing together researchers in computational genomics and bioinformatics to discuss new frontiers in gene sequencing.
