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Reference Sequence Resource!
By LEGE 1636 days agowww.encodeproject.org - The ENCODE project uses Reference Genomes from NCBI or UCSC to provide a consistent framework for mapping high-throughput sequencing data. In general, ENCODE data are mapped consistently to 2 human (GRCH38, hg19) and 2 mouse...Large Language Models in Bioinformatics: Transforming Data Analysis and Interpretation
By LEGE 431 days agoThe integration of artificial intelligence (AI) into bioinformatics has ushered in a new era of computational biology. Among the most transformative advancements are large language models (LLMs), such as GPT and BERT, which leverage deep learning to...A Post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs
By Abhimanyu Singh 3223 days agowww.sanger.ac.uk - PAGIT addresses the need for software to generate high quality draft genomes. It is based on a series of programs that we developed: ABACAS, that is able to contiguate contigs from a de novo assembly against a closely related reference. IMAGE, an...Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
By Rahul Nayak 3038 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 3018 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 2862 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...NextSV: a meta-caller for structural variants from low-coverage long-read sequencing data
By Jit 2772 days agogithub.com - NextSV, a meta SV caller and a computational pipeline to perform SV calling from low coverage long-read sequencing data. NextSV integrates three aligners and three SV callers and generates two integrated call sets (sensitive/stringent) for different...BamView: a free interactive display of read alignments in BAM data files
By Neel 2677 days agobamview.sourceforge.net - To run the application on UNIX from the downloaded jar file run the UNIX: java -mx512m -jar BamView.jar and extra command line options are given when '-h' is used: java -jar BamView.jar -h BAM files can be specified on the command line with the...ZENBU: a collaborative, omics data integration and interactive visualization system
By BioJoker 2621 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 2537 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...
