<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/1161?offset=1440 https://bioinformaticsonline.com/bookmarks/view/29410/entrez-direct-e-utilities-on-the-unix-command-line Wed, 19 Oct 2016 08:06:24 -0500 https://bioinformaticsonline.com/bookmarks/view/29410/entrez-direct-e-utilities-on-the-unix-command-line <![CDATA[Entrez Direct: E-utilities on the UNIX Command Line]]> Entrez Direct (EDirect) is an advanced method for accessing the NCBI's suite of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from a UNIX terminal window. Functions take search terms from command-line arguments. Individual operations are combined to build multi-step queries. Record retrieval and formatting normally complete the process.

EDirect also provides an argument-driven function that simplifies the extraction of data from document summaries or other results that are returned in structured XML format. This can eliminate the need for writing custom software to answer ad hoc questions. Queries can move seamlessly between EDirect commands and UNIX utilities or scripts to perform actions that cannot be accomplished entirely within Entrez.

Address of the bookmark: https://www.ncbi.nlm.nih.gov/books/NBK179288/

]]> Anjana https://bioinformaticsonline.com/bookmarks/view/29500/genomescope-open-source-web-tool-to-rapidly-estimate-the-overall-characteristics-of-a-genome-including-genome-size-heterozygosity-rate-and-repeat-content-from-unprocessed-short-reads Fri, 21 Oct 2016 05:46:43 -0500 https://bioinformaticsonline.com/bookmarks/view/29500/genomescope-open-source-web-tool-to-rapidly-estimate-the-overall-characteristics-of-a-genome-including-genome-size-heterozygosity-rate-and-repeat-content-from-unprocessed-short-reads <![CDATA[GenomeScope: open-source web tool to rapidly estimate the overall characteristics of a genome, including genome size, heterozygosity rate, and repeat content from unprocessed short reads]]>

Summary: GenomeScope is an open-source web tool to rapidly estimate the overall characteristics of a genome, including genome size, heterozygosity rate, and repeat content from unprocessed short reads. These features are essential for studying genome evolution, and help to choose parameters for downstream analysis. We demonstrate its accuracy on 324 simulated and 16 real datasets with a wide range in genome sizes, heterozygosity levels, and error rates. Availability and Implementation: http://qb.cshl.edu/genomescope/, https://github.com/schatzlab/genomescope.git

Address of the bookmark: http://qb.cshl.edu/genomescope/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/29578/plink2 Thu, 27 Oct 2016 11:24:45 -0500 https://bioinformaticsonline.com/bookmarks/view/29578/plink2 <![CDATA[PLINK2]]> This is a comprehensive update to Shaun Purcell's PLINK command-line program, developed by Christopher Chang with support from the NIH-NIDDK's Laboratory of Biological Modeling, the Purcell Lab at Mount Sinai School of Medicine, and others. (What's new?) (Credits.) (Methods paper.)

Address of the bookmark: https://www.cog-genomics.org/plink2/

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