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assembler, assembly, PASA, Gene, Structure, Annotation, Analysis, Ra, de novo, DNA, third, generation, sequencing, genome, Carefully, opt, human, reference, Best, Practices, Variant, Calling, GATK, VICUNA, software, tool, enables, consensus, ultra-deep, sequence, diverse, viral, heterogeneous, populations, graph, builder, pangenome, pggb, tutorial, book, workbook, bioinformatics, learn
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bioinformatics workbook
By biogeek 1207 days agobioinformaticsworkbook.org - This books assumes that the reader has some knowledge of biology and basic understanding of the Unix command line. However, for the beginner, the appendix contains introductory material and tips/tricks for common bioinformatic problems, that is...pggb: the pangenome graph builder
By biogeek 1321 days agogithub.com - This pangenome graph construction pipeline renders a collection of sequences into a pangenome graph (in the variation graph model). Its goal is to build a graph that is locally directed and acyclic while preserving large-scale variation. Maintaining...VICUNA: a software tool that enables consensus assembly of ultra-deep sequence derived from diverse...
By biogeek 1341 days agowww.broadinstitute.org - VICUNA is a de novo assembly program targeting populations with high mutation rates. It creates a single linear representation of the mixed population on which intra-host variants can be mapped. For clinical samples rich in...Best Practices for Variant Calling with the GATK
By biogeek 1526 days agowww.broadinstitute.org - The presentations below were filmed during the March 2015 GATK Workshop, part of the BroadE Workshop series. At the time of this workshop, the current version of Broad’s Genome Analysis Toolkit (GATK) was version...Carefully opt for human reference genome
By biogeek 1530 days agolh3.github.io - Heng Li posted several issues with the human reference genomes given in these resources and suggests the following compressed FASTA file to be used as hg38/GRCh38 human reference genome. if you map reads to GRCh38 or hg38, use the...Ra assembler - a de novo DNA assembler for third generation sequencing data
By biogeek 2312 days agogithub.com - Integration of the Ra assembler - a de novo DNA assembler for third generation sequencing data developed on Faculty of Electrical Engineering and Computing (FER), Ruder Boskovic Institute (RBI) and Genome Institute of Singapore (GIS). Ra is in...PASA: Gene Structure Annotation and Analysis
By biogeek 2313 days agopasapipeline.github.io - PASA, acronym for Program to Assemble Spliced Alignments, is a eukaryotic genome annotation tool that exploits spliced alignments of expressed transcript sequences to automatically model gene structures, and to maintain gene structure annotation...
