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FinisherSC:a repeat-aware tool for upgrading de novo assembly using long reads
By Jit 2288 days agogithub.com - Here is the command to run the tool: python finisherSC.py destinedFolder mummerPath If you are running on server computer and would like to use multiple threads, then the following commands can generate 20 threads to run FinisherSC. python...ECTOOLS: Long Read Correction and other Correction tools
By Jit 2515 days agogithub.com - Long Read Correction and other Correction tools This package is a loose collection of scripts. To run the correctionroutine see the section below. Descriptions of the other scriptsare at the bottom of this file. Contact: gurtowsk@cshl.edu In...1mb long DNA with Nanopore technology
By Jit 2532 days agoLongest read of 1mb achievements with NanoporeLoRMA: a tool for correcting sequencing errors in long reads such those produced by Pacific...
By Jit 3084 days agowww.cs.helsinki.fi - LoRMA is a tool for correcting sequencing errors in long reads such those produced by Pacific Biosciences sequencing machines. Publication: L. Salmela, R. Walve, E. Rivals, and E. Ukkonen: Accurate selfcorrection of errors in long reads using de...MetaGraph: Ultra Scalable Framework for DNA Search, Alignment, Assembly
By Abhi 169 days agometagraph.ethz.ch - The MetaGraph framework is designed to work with a wide range of input data sets, indexing from a few samples up to the contents of entire archives with hundreds of thousands of records. The indexing workflow always follows the same principle,...MUMmer4: A fast and versatile genome alignment system
By Jit 2486 days agomummer4.github.io - MUMmer4, a substantially improved version of MUMmer that addresses genome size constraints by changing the 32-bit suffix tree data structure at the core of MUMmer to a 48-bit suffix array, and that offers improved speed through parallel processing...AlignQC: A tool for assessing an alignment, and generating reports that are easy to share
By Jit 2301 days agowww.healthcare.uiowa.edu - Long read alignment analysis. Generate a reports on sequence alignments for mappability vs read sizes, error patterns, annotations and rarefraction curve analysis. The most basic analysis only requires a BAM file, and outputs a web browser...Shouji: a fast and efficient pre-alignment filter for sequence alignment
By Jit 1847 days agogithub.com - The ability to generate massive amounts of sequencing data continues to overwhelm the processing capacity of existing algorithms and compute infrastructures. In this work, we explore the use of hardware/software co-design and hardware acceleration...poRe: an R package for the visualization and analysis of nanopore sequencing data
By Jit 2558 days ago Comments (1)academic.oup.com - Motivation: The Oxford Nanopore MinION device represents a unique sequencing technology. As a mobile sequencing device powered by the USB port of a laptop, the MinION has huge potential applications. To enable these applications, the...GPOPSIM: a simulation tool for whole-genome genetic data
By Jit 2503 days agogithub.com - GPOPSIM is a simulation tool for pedigree, phenotypes, and genomic data, with a variety of population and genome structures and trait genetic architectures. It provides flexible parameter settings for a wide discipline of users, especially can...
