BioJoker
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parallelLastz: Lastz with multi-threads support.
By BioStar 1555 days agogithub.com - Running Lastz (https://github.com/lastz/lastz) in parallel mode. This program is for single computer with multiple core processors. When the query file format is fasta, you can specify many threads to process it. It can reduce run time linearly,...Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
By Rahul Nayak 2568 days agogithub.com - Automatic Filtering, Trimming, Error Removing and Quality Control for fastq dataAfterQC can simply go through all fastq files in a folder and then output three folders: good, bad and QC folders, which contains good...MinION_GC: An R script to do some QC on MinION data
By Radha Agarkar 2548 days agogithub.com - Other tools focus on getting data out of the fastq or fast5 files, which is slow and computationally intensive. The benefit of this approach is that it works on a single, small, .txt summary file. So it's a lot quicker than most other things out...MIX: Combining multiple assemblies from NGS data
By Rahul Nayak 2392 days agogithub.com - Mix is a tool that combines two or more draft assemblies, without relying on a reference genome and has the goal to reduce contig fragmentation and thus speed-up genome finishing. The proposed algorithm builds an extension graph where vertices...ZENBU: a collaborative, omics data integration and interactive visualization system
By BioJoker 2151 days agofantom.gsc.riken.jp - ZENBU is a data integration, data analysis, and visualization system enhanced for RNAseq, ChipSeq, CAGE and other types of next-generation-sequence-tag (NGS) based data. ZENBU allows for novel data exploration through "on-demand" data...OMTools: a software package for visualizing and processing optical mapping data
By BioJoker 2067 days agogithub.com - OMTools, an efficient and intuitive data processing and visualization suite to handle and explore large-scale optical mapping profiles. OMTools includes modules for visualization (OMView), data processing and simulation. These modules together form...pbmm2:A minimap2 frontend for PacBio native data formats
By BioStar 1741 days agogithub.com - pbmm2 is a SMRT C++ wrapper for minimap2's C API. Its purpose is to support native PacBio in- and output, provide sets of recommended parameters, generate sorted output on-the-fly, and postprocess alignments. Sorted output can be used directly for...PLAR: Pipeline for lncRNA annotation from RNA-seq data
By Abhi 1052 days agowww.weizmann.ac.il - Due to several requests, we are releasing an assingment of orthologs, determined using the same methods used in Hezroni et al. (BLAST, Whole Genome Alignment (WGA), and synteny). One is comparing human GENCODE genes (from GENCODE v30) to lncRNAs...Creating Genetic Maps from GBS data
By BioStar 443 days agobioinformaticsworkbook.org - Genetic map, as the name suggest is simply knowing the relative positions of specific sequences across the genome. There are various methods to generate them, but most popular method is to use a cross between the known parents and examining their...Managing and Analyzing Next-Generation Sequence Data
By Rahul Agarwal 3851 days agowww.ploscompbiol.org - Centralized Bioinformatics Core Facilities provide shared resources for the computational and IT requirements of the investigators in their department or institution. As such, they must be able to effectively react to new types of experimental...
