RGFA: powerful and convenient handling of assembly graphs
...A typical application of RGFA is the editing of a graph, to finish the assembly of a sequence, using informat...not available to the assembler. We illustrate a use case, in which the assembly of a repetitive metagenomic f...1574 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://geno...2286 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...2265 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 demo2265 days ago
PLAR: Pipeline for lncRNA annotation from RNA-seq data
...aring human GENCODE genes (from GENCODE v30) to lncRNAs from other species identified by PLAR. Available here. Species Assembly Code Transcriptome...856 days ago
ARCS: scaffolding genome drafts with linked reads
...ssemblies. We show how the contiguity of an ABySS H.sapiensgenome assembly can be increased over six-fol...ed in linked read data for connecting high-quality sequences in genome assembly drafts.2258 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 scaffolds). The join between two contigs A and B is c...2243 days ago
SciLifeLab tutorial for bioinformatics analysis !
...uary - Uppsala Introduction to Genome Annotation 2015 April - Uppsala2016 April - Uppsala2017 April - Uppsala2018 May - Uppsala De Novo Genome Assembly 2016 November - Uppsala2017...2217 days ago
AlignGraph: algorithm for secondary de novo genome assembly guided by closely related references
...ingContig remainingContigs.fa [--kMer k --insertVariation insertVariation --coverage coverage --part p --fastMap --ratioCheck --iterativeMap --misassemblyRemoval --resume]2216 days ago
ALPACA: A hybrid strategy for assembly of genomic DNA shotgun sequencing reads.
ALPACA requires Celera Assembler 8.3 or later. It is recommended to build Celera Assembler from source. (Why? The pre-built binaries CA_8.3rc1 and CA8.3rc2 will work for any large data set. Detail paper at https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-3927-82204 days ago