ECTOOLS: Long Read Correction and other Correction tools
Long Read Correction and other Correction tools This package is a loose collection o...short, the correction algorithm takes as input the unitigs from a short read assembly and uses them to correct long...2340 days ago
RGFA: powerful and convenient handling of assembly graphs
RGFA, an implementation of the proposed GFA specification...n of RGFA is the editing of a graph, to finish the assembly of a sequence, using informat...assembler. We illustrate a use case, in which the assembly of a repetitive metagenomic f...1595 days ago
HINGE: Long-Read Assembly Achieves Optimal Repeat Resolution
Software accompanying "HINGE: Long-Read Assembly Achieves Optimal Repeat Resolution" Preprint: http://biorxiv.org/content/early/2016/08/01/062117 Paper: http://genome.cs...2307 days ago
Genome assembly stats plotting
A de novo genome assembly can be summarised b y a number...f metrics, including: Overall assembly length Number of scaffolds/c...ntig Scaffold/contig N50 and N90Assembly base composition, in particul...at summarises most commonly used assembly metrics in a single visualisa...2286 days ago
Generate interactive codon usage plots
Generate interactive codon usage plots as used at ensembl.lepbase.org. The input file format can be generated from an Ensembl database using the export_json.pl script from the easy-import pipeline. live demo2286 days ago
PLAR: Pipeline for lncRNA annotation from RNA-seq data
Due to several requests, we are releasing an assingment of orthologs, determined usin...pecies identified by PLAR. Available here. Species Assembly Code Transcriptome...877 days ago
ARCS: scaffolding genome drafts with linked reads
ARCS, an application that utilizes the barcoding informati...ow the contiguity of an ABySS H.sapiensgenome assembly can be increased over six-fol...ta for connecting high-quality sequences in genome assembly drafts.2280 days ago
repeat-aware: Repeat aware scaffolding evaluation framework by Igor Mandric
Genome scaffolding is a classical challenging problem in bioinformatics. It refers to joining assembly contigs into chains (called s...2265 days ago
SciLifeLab tutorial for bioinformatics analysis !
SciLifeLab is a national center for molecular biosciences with focus on health and en...ala2016 April - Uppsala2017 April - Uppsala2018 May - Uppsala De Novo Genome Assembly 2016 November - Uppsala2017...2238 days ago
AlignGraph: algorithm for secondary de novo genome assembly guided by closely related references
AlignGraph is a software that extends and joins contigs or scaffolds by reassembling...ation --coverage coverage --part p --fastMap --ratioCheck --iterativeMap --misassemblyRemoval --resume]2238 days ago