NanoSim: nanopore sequence read simulator based on statistical characterization.
NanoSim, a fast and scalable read simulator that ca...y-specific features of ONT data and allows for adjustments upon i...ensive alignment-based analysis and generates a set of read profi...e. NanoSim is written in Python and R. The source files and manua...e at the Genome Sciences Centre website: ht...2327 days ago
Building Web UIs With Mojolicious Perl
Mojolicious is one of 3 leading web frame...perl ecosystem (along with Dancer and Catalyst) and by far my favorite. Mojolici...ous aims to provide a complete web development experience. It thus h...ependencies, comes with a built-in development and production server and many other feat...2318 days ago
Ra assembler - a de novo DNA assembler for third generation sequencing data
Integration of the Ra assembler - a de n...Faculty of Electrical Engineering and Computing (FER), Ruder Boskovic Institute (RBI) and Genome Institute of Singapore (GIS). Ra is in development since 2014 in the for...g overlaps using a very sensitive and specific overlapper ("graphmap -w owl...2317 days ago
mojolicious: a next generation web framework for the Perl programming language.
Back in the early days of the web, m...owing much about the language and powerful enough to keep you g...RESTful routes, plugins, commands, Perl-ish templates, content...ver. A powerful web development toolkit, that you can...framework. Full stack HTTP and WebSocket client/server implementatio...2302 days ago
An Introduction to Applied Bioinformatics
IAB is primarily being developed by Greg Caporaso(GitHub/Twitter: @gregcaporaso) in the&...find information on the courses I teach on my teaching website and information on my research and lab on my lab website. &...2253 days ago
UCSC SARS-CoV-2 Genome Browser
The UCSC SARS-CoV-2 Genome Browser (https://...us, containing many annotation tracks and new features, including conse...iruses, immune epitopes, RT–PCR and sequencing primers and CRISPR...s resource to accelerate research and development activities globally.847 days ago
Multi-CAR: a tool of contig scaffolding using multiple references
we design a simple heuristic method to further revise our single refere...s references to more accurately order and orient the contigs of a draft...genetic relationships among the draft and reference genomes and librari...erence-based scaffolding tools Ragout and MeDuSa....2249 days ago
SEX-DETector: A Probabilistic Approach to Study Sex Chromosomes in Non-Model Organisms
SEX-DETector is a probabilistic method tha...n RNAseq data from a cross (parents and progeny of each sex) to infer autosomal and sex-linked genes (genes locat...g data can be used for the assembly and for the mapping of the reads....le for download on the PopPhyl website) as...2164 days ago
2179 days ago
CoLoRMap: Correcting Long Reads by Mapping short reads
Second generation sequencing technol...ads are difficult to assemble and often lead to highly fragmented assemblies. The recent developments in long reads sequen...coverage. This motivates the development of hybrid approaches that lev...the edit score to a long read and extending corrected regions by local...2082 days ago