Jit
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Interview Mark Sansom (U. Oxford): Simulations of Membrane Proteins
By Shreya Ganguli 4095 days agoWorkshop in Bioinformatics, 4/June/2012 Campus Vida's Research Centers organize in Santiago de Compostela the Workshop in Bioinformatics. This event addressed issues such as structural bioinformatics, biological modelling and mining bioinformatics...Postdoctoral Fellowship at Department of Psychiatry, Warneford Hospital, Oxford
Applications are invited for a postdoctoral research assistant to work in the Translational Neuroscience and Dementia Research Group (TNDRG) on a project using informatics approaches to understand and prevent dementia, specifically on the role of...miniasm: very fast OLC-based de novo assembler for noisy long reads
By Jit 2583 days agogithub.com - Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format. Different from mainstream...ARCS: scaffolding genome drafts with linked reads
By Rahul Nayak 2484 days agogithub.com - ARCS, an application that utilizes the barcoding information contained in linked reads to further organize draft genomes into highly contiguous assemblies. We show how the contiguity of an ABySS H.sapiensgenome assembly can be increased over...MECAT: fast mapping, error correction, and de novo assembly for single-molecule sequencing reads
By Rahul Nayak 2418 days agogithub.com - MECAT is an ultra-fast Mapping, Error Correction and de novo Assembly Tools for single molecula sequencing (SMRT) reads. MECAT employs novel alignment and error correction algorithms that are much more efficient than the state of art of aligners and...Jvarkit : Java utilities for Bioinformatics
By Jit 2390 days agolindenb.github.io - Collection of Java tool kits for bioinformatics works: Jvarkit : Java utilities for BioinformaticsEAGLER: a scaffolding tool for long reads.
By Jit 2394 days agogithub.com - EAGLER is a scaffolding tool for long reads. The scaffolder takes as input a draft genome created by any NGS assembler and a set of long reads. The long reads are used to extend the contigs present in the NGS draft and possibly join overlapping...ReMILO: reference assisted misassembly detection algorithm using short and long reads.
By Jit 2362 days agogithub.com - ReMILO, a reference assisted misassembly detection algorithm that uses both short reads and PacBio SMRT long reads. ReMILO aligns the initial short reads to both the contigs and reference genome, and then constructs a novel data structure called...Hercules: a profile HMM-based hybrid error correction algorithm for long reads
By Jit 2317 days agogithub.com - Choosing whether to use second or third generation sequencing platforms can lead to trade-offs between accuracy and read length. Several studies require long and accurate reads including de novo assembly, fusion and structural variation detection....LoRMA: A tool for correcting sequencing errors in long reads
By Abhimanyu Singh 2300 days agogite.lirmm.fr - An error correction method that uses long reads only. The method consists of two phases: first, we use an iterative alignment-free correction method based on de Bruijn graphs with increasing length of k-mers, and second, the corrected reads are...
