<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/43902?offset=310 https://bioinformaticsonline.com/bookmarks/view/34594/synima-synteny-imaging-tool Sun, 10 Dec 2017 17:03:48 -0600 https://bioinformaticsonline.com/bookmarks/view/34594/synima-synteny-imaging-tool <![CDATA[Synima: Synteny Imaging tool]]> Synteny Imaging tool (Synima) written in Perl, which uses the graphical features of R. Synima takes orthologues computed from reciprocal best BLAST hits or OrthoMCL, and DAGchainer, and outputs an overview of genome-wide synteny in PDF. Each of these programs are included with the Synima package, and a pipeline for their use. Synima has a range of graphical parameters including size, colours, order, and labels, which are specified in a config file generated by the first run of Synima – and can be subsequently edited. Synima runs quickly on a command line to generate informative and publication quality figures. Synima is open source and freely available from https://github.com/rhysf/Synima under the MIT License.

Address of the bookmark: https://github.com/rhysf/Synima

]]> Jit https://bioinformaticsonline.com/bookmarks/view/36271/heap-a-highly-sensitive-and-accurate-snp-detection-tool-for-low-coverage-high-throughput-sequencing-data Thu, 19 Apr 2018 08:06:03 -0500 https://bioinformaticsonline.com/bookmarks/view/36271/heap-a-highly-sensitive-and-accurate-snp-detection-tool-for-low-coverage-high-throughput-sequencing-data <![CDATA[Heap: a highly sensitive and accurate SNP detection tool for low-coverage high-throughput sequencing data]]> Heap, that enables robustly sensitive and accurate calling of SNPs, particularly with a low coverage NGS data, which must be aligned to the reference genome sequences in advance. To reduce false positive SNPs, Heap determines genotypes and calls SNPs at each site except for sites at the both end of reads or containing a minor allele supported by only one read. Performance comparison with existing tools showed that Heap achieved the highest F-scores with low coverage (7X) restriction-site associated DNA sequencing reads of sorghum and rice individuals. This will facilitate cost-effective GWAS and GP studies in this NGS era. Code and documentation of Heap are freely available from https://github.com/meiji-bioinf/heap and our web site (http://bioinf.mind.meiji.ac.jp/lab/en/tools.html).

Address of the bookmark: https://github.com/meiji-bioinf/heap

]]> Jit https://bioinformaticsonline.com/bookmarks/view/36812/porechop-tool-for-finding-and-removing-adapters-from-oxford-nanopore-reads Tue, 29 May 2018 07:33:44 -0500 https://bioinformaticsonline.com/bookmarks/view/36812/porechop-tool-for-finding-and-removing-adapters-from-oxford-nanopore-reads <![CDATA[Porechop: tool for finding and removing adapters from Oxford Nanopore reads]]> Porechop is a tool for finding and removing adapters from Oxford Nanopore reads. Adapters on the ends of reads are trimmed off, and when a read has an adapter in its middle, it is treated as chimeric and chopped into separate reads. Porechop performs thorough alignments to effectively find adapters, even at low sequence identity.

Porechop also supports demultiplexing of Nanopore reads that were barcoded with the Native Barcoding Kit, PCR Barcoding Kit or Rapid Barcoding Kit.

Address of the bookmark: https://github.com/rrwick/Porechop

]]> Rahul Nayak https://bioinformaticsonline.com/bookmarks/view/36905/d-genies-a-tool-for-dotplot-large-genomes-in-an-interactive-efficient-and-simple-way Mon, 11 Jun 2018 09:41:22 -0500 https://bioinformaticsonline.com/bookmarks/view/36905/d-genies-a-tool-for-dotplot-large-genomes-in-an-interactive-efficient-and-simple-way <![CDATA[D-GENIES: A tool for Dotplot large Genomes in an Interactive, Efficient and Simple way]]> Address of the bookmark: http://dgenies.toulouse.inra.fr/

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