<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/43427?offset=440 https://bioinformaticsonline.com/file/view/42559/sample-bandage-input-file-for-visual-analysis Wed, 06 Jan 2021 03:51:50 -0600 https://bioinformaticsonline.com/file/view/42559/sample-bandage-input-file-for-visual-analysis <![CDATA[Sample bandage input file for visual analysis]]> Sample bandage input file for visual analysis ...

]]> Jit https://bioinformaticsonline.com/blog/view/42166/software-for-genome-assembly Sun, 30 Aug 2020 09:51:38 -0500 https://bioinformaticsonline.com/blog/view/42166/software-for-genome-assembly <![CDATA[Software for genome assembly !]]> List of bioinformatics tools/Software Website References for genome assembly:

1 Falcon https://github.com/PacificBiosciences/pb-assembly

2 Canu assembler http://canu.readthedocs.io/en/latest/index.html

3 Miniasm assembler https://github.com/lh3/miniasm

4 PBJelly scaffolding tool https://sourceforge.net/projects/pb-jelly/

5 ARCS scaffolding tool https://github.com/bcgsc/arcs

6 Redundans reduction and scaffolding tool https://github.com/Gabaldonlab/redundans

7 Arrow error correction https://github.com/PacificBiosciences/ GenomicConsensus

8 PILON error correction https://github.com/broadinstitute/pilon/wiki

9 BUSCO single copy gene markers http://busco.ezlab.org/

10 Bandage graph assembly viewer https://rrwick.github.io/Bandage/

11 Gepard dotter http://cube.univie.ac.at/gepard

12 MUMmer aligner and plotter http://mummer.sourceforge.net/

]]> LEGE https://bioinformaticsonline.com/bookmarks/view/42923/flanker Sat, 27 Feb 2021 22:04:53 -0600 https://bioinformaticsonline.com/bookmarks/view/42923/flanker <![CDATA[Flanker]]> Flanker, a Python package which performs alignment-free clustering of gene flanking sequences in a consistent format, allowing investigation of mobile genetic elements (MGEs) without prior knowledge of their structure. Flanker can be flexibly parameterised to finetune outputs by characterising upstream and downstream regions separately and investigating variable lengths of flanking sequence.

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Address of the bookmark: https://github.com/wtmatlock/flanker

]]> Rahul Nayak https://bioinformaticsonline.com/bookmarks/view/43088/iva-accurate-de-novo-assembly-of-rna-virus-genomes Wed, 23 Jun 2021 07:51:59 -0500 https://bioinformaticsonline.com/bookmarks/view/43088/iva-accurate-de-novo-assembly-of-rna-virus-genomes <![CDATA[IVA: accurate de novo assembly of RNA virus genomes]]> IVA (Iterative Virus Assembler) designed specifically for read pairs sequenced at highly variable depth from RNA virus samples. We tested IVA on datasets from 140 sequenced samples from human immunodeficiency virus-1 or influenza-virus-infected people and demonstrated that IVA outperforms all other virus de novo assemblers.

Availability and implementation: The software runs under Linux, has the GPLv3 licence and is freely available from http://sanger-pathogens.github.io/iva

https://pubmed.ncbi.nlm.nih.gov/25725497/

Address of the bookmark: https://github.com/sanger-pathogens/iva

]]> Neel https://bioinformaticsonline.com/bookmarks/view/43364/ragtag-a-collection-of-software-tools-for-scaffolding-and-improving-modern-genome-assemblies Sat, 11 Sep 2021 00:28:14 -0500 https://bioinformaticsonline.com/bookmarks/view/43364/ragtag-a-collection-of-software-tools-for-scaffolding-and-improving-modern-genome-assemblies <![CDATA[RagTag: a collection of software tools for scaffolding and improving modern genome assemblies]]> RagTag is a collection of software tools for scaffolding and improving modern genome assemblies. Tasks include:

Address of the bookmark: https://github.com/malonge/RagTag

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