<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/44587?offset=20 https://bioinformaticsonline.com/bookmarks/view/44529/contigextender-a-new-approach-to-improving-de-novo-sequence-assembly-for-viral-metagenomics-data Wed, 08 May 2024 07:32:45 -0500 https://bioinformaticsonline.com/bookmarks/view/44529/contigextender-a-new-approach-to-improving-de-novo-sequence-assembly-for-viral-metagenomics-data <![CDATA[ContigExtender: a new approach to improving de novo sequence assembly for viral metagenomics data]]> ContigExtender, was developed to extend contigs, complementing de novo assembly. ContigExtender employs a novel recursive Overlap Layout Candidates (r-OLC) strategy that explores multiple extending paths to achieve longer and highly accurate contigs. ContigExtender is effective for extending contigs significantly in in silico synthesized and real metagenomics datasets.

More at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7953547/

extension process

Address of the bookmark: https://github.com/dengzac/contig-extender

]]> LEGE https://bioinformaticsonline.com/bookmarks/view/28805/bambus Tue, 16 Aug 2016 08:09:15 -0500 https://bioinformaticsonline.com/bookmarks/view/28805/bambus <![CDATA[Bambus]]>

Bambus 2.0, the second generation Bambus scaffolder available as an open source package. While most other scaffolders are closely tied to a specific assembly program, Bambus accepts the output from most current assemblers and provides the user with great flexibility in choosing the scaffolding parameters. In particular, Bambus is able to accept contig linking data other than specified by mate-pairs. Such sources of information include alignment to a reference genome (Bambus can directly use the output of MUMmer), physical mapping data, or information about gene synteny.

Address of the bookmark: https://www.cbcb.umd.edu/software/bambus2

]]> Jit https://bioinformaticsonline.com/opportunity/view/40771/coordinator-of-bioinformatics-core-facility-robert-koch-institute-berlin Thu, 30 Jan 2020 07:01:45 -0600 <![CDATA[Coordinator of Bioinformatics Core Facility-Robert Koch Institute Berlin]]> We are offering the following position in unit MF 1 "Bioinformatics" of department MF "Methodology and Research Infrastructure" for a

Coordinator of our Bioinformatics Core Facility (all genders)

(salary dependent on qualifications and experience in accordance with public sector wage scale [TVöD] up to grade E 14).

The contract is not limited. The position will be available immediately.
https://www.researchgate.net/job/938589_Coordinator_of_our_Bioinformatics_Core_Facility_all_genders

]]> https://bioinformaticsonline.com/bookmarks/view/42139/mixtures-a-novel-tool-for-bacterial-strain-reconstruction-from-reads Fri, 21 Aug 2020 08:23:19 -0500 https://bioinformaticsonline.com/bookmarks/view/42139/mixtures-a-novel-tool-for-bacterial-strain-reconstruction-from-reads <![CDATA[mixtureS: a novel tool for bacterial strain reconstruction from reads]]>

mixtureS that can de novo identify bacterial strains from shotgun reads of a clonal or metagenomic sample, without prior knowledge about the strains and their variations. Tested on 243 simulated datasets and 195 experimental datasets, mixtureS reliably identified the strains, their numbers and their abundance. Compared with three tools, mixtureS showed better performance in almost all simulated datasets and the vast majority of experimental datasets.

Availability

The source code and tool mixtureS is available at http://www.cs.ucf.edu/˜xiaoman/mixtureS/.

Address of the bookmark: http://www.cs.ucf.edu/~xiaoman/mixtureS/

]]> BioStar