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SALSA: A tool to scaffold long read assemblies with Hi-C
By Jit 2823 days agogithub.com - This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branch. To use the latest version,...Referee: Genome assembly quality scores
By Jit 2680 days agogwct.github.io - Modern genome sequencing technologies provide a succint measure of quality at each position in every read, however all of this information is lost in the assembly process. Referee summarizes the quality information from the reads that map to a site...Genome Annotation using MAKER tutorial !
By Shruti Paniwala 2634 days agowww.biostars.org - MAKER is a great tool for annotating a reference genome using empirical and ab initiogene predictions. GMOD, the umbrella organization that includes MAKER, has some nice tutorials online for running MAKER. However, these were quite...Genome assembly forensics: finding the elusive mis-assembly
By Jit 2597 days agoamos.sourceforge.net - We present the first collection of tools aimed at automated genome assembly validation. This work formalizes several mechanisms for detecting mis-assemblies, and describes their implementation in our automated validation pipeline,...gEVAL: Genome Evaluation Browser
By Jit 2455 days agogeval.sanger.ac.uk - The gEVAL Browser allows the evaluation of genome assemblies through its tools and pre-computed analyses. The strength of this browser is the ability to navigate an up to date assembly and identify problematic regions and assist in...De novo Genome Assembly for Illumina Data
By Rahul Nayak 2239 days agowww.melbournebioinformatics.org.au - Written and maintained by Simon Gladman - Melbourne Bioinformatics (formerly VLSCI) Protocol Overview / Introduction In this protocol we discuss and outline the process of de novo assembly for small to medium sized...Protocol for De novo Genome Assembly using Illumina Reads
By BioStar 1876 days agoIn this protocol, we address and describe the de novo assembly method for small to medium-sized genomes.Genome Assembly Workshop 2020
By Jit 1656 days agoucdavis-bioinformatics-training.github.io - Our team offers custom bioinformatics services to academic and private organizations. We have a strong academic background with a focus on cutting edge, open source software. We replicate standard analysis pipelines (best practices) when...Peregrine & SHIMMER Genome Assembly Toolkit
By Abhi 1543 days agogithub.com - Peregrine is a fast genome assembler for accurate long reads (length > 10kb, accuracy > 99%). It can assemble a human genome from 30x reads within 20 cpu hours from reads to polished consensus. It uses Sparse HIereachical MimiMizER (SHIMMER)...HIV genome database !
By Rahul Nayak 1507 days agowww.hiv.lanl.gov - HIV resources https://www.hiv.lanl.gov/components/sequence/HIV/search/search.html
