Computational Genomics
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Rescooped by RickLStevens from Embedded Systems News
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How to Read OpenOffice / LibreOffice Files from the Command Line

How to Read OpenOffice / LibreOffice Files from the Command Line | Computational Genomics | Scoop.it
Let’s say you have edited a file in LibreOffice Writer, but later you access your computer remotely via SSH for example. You don’t really want to bother copying the file to your current...

Via cnxsoft
RickLStevens's insight:

this is very useful.  I've been wanting something like this for a while.

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Convey Computers Implementation of PacBioToCA Algorithm Speeds DNA ... - IT Business Net

“Convey Computers Implementation of PacBioToCA Algorithm Speeds DNA ... IT Business Net Last year, Dr.”
RickLStevens's insight:
Nice pairing of two emerging technologies. Convey has a very exciting roadmap.
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Rescooped by RickLStevens from Bioinformatics Software: Sequence Analysis
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YOKOFAKUN: Inside Jvarkit: view BAM, cut, stats, head, tail, shuffle, downsample, group-by-gene VCFs...

YOKOFAKUN: Inside Jvarkit: view BAM, cut, stats, head, tail, shuffle, downsample, group-by-gene VCFs... | Computational Genomics | Scoop.it

Via Mel Melendrez-Vallard
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Rescooped by RickLStevens from Bioinformatics Software: Sequence Analysis
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Next-Generation Sequence Assembly: Four Stages of Data Processing and Computational Challenges

Next-Generation Sequence Assembly: Four Stages of Data Processing and Computational Challenges | Computational Genomics | Scoop.it
“ by Sara El-Metwally, Taher Hamza, Magdi Zakaria, Mohamed Helmy Decoding DNA symbols using next-generation sequencers was a major breakthrough in genomic research.”
Via Mel Melendrez-Vallard
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Rescooped by RickLStevens from Bioinformatics Software: Sequence Analysis
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Pathoscope: Species identification and strain attribution with unassembled sequencing data

Pathoscope: Species identification and strain attribution with unassembled sequencing data | Computational Genomics | Scoop.it
“ An international, peer-reviewed genome sciences journal featuring outstanding original research that offers novel insights into the biology of all organisms”
Via Mel Melendrez-Vallard
RickLStevens's insight:
Need to compare to RAIphy and others.
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Rescooped by RickLStevens from Plant Breeding and Genomics News
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Sequence Comparative Analysis Using Networks: Software for Evaluating De Novo Transcript Assembly from Next-Generation Sequencing

DNA sequencing technology is becoming more accessible to a variety of researchers as costs continue to decline. As researchers begin to sequence novel transcriptomes, most of these data sets lack a reference genome and will have to rely on de novo assemblers. Making comparisons across assemblies can be difficult: each program has its strengths and weaknesses, and no tool exists to comparatively evaluate these data sets. We developed software in R, called Sequence Comparative Analysis using Networks (SCAN), to perform statistical comparisons between distinct assemblies. SCAN uses a reference data set to identify the most accurate de novo assembly and the “good” transcripts in the user’s data. We tested SCAN on three publicly available transcriptomes, each assembled using three assembly programs. Moreover, we sequenced the transcriptome of the oomycete Achlya hypogyna and compared de novo assemblies from Velvet, ABySS, and the CLC Genomics Workbench assembly algorithms. One thousand one hundred twenty-eight of the CLC transcripts were statistically similar to the reference, compared with 49 of the Velvet transcripts and 937 of the ABySS transcripts. SCAN’s strength is providing statistical support for transcript assemblies in a biological context. However, SCAN is designed to compare distinct node sets in networks, therefore it can also easily be extended to perform statistical comparisons on any network graph regardless of what the nodes represent.
Via Plant Breeding and Genomics News
RickLStevens's insight:
I'd like to integrate things like BayesDB with this.
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Rescooped by RickLStevens from Bioinformatics Software: Sequence Analysis
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SRComp: Short Read Sequence Compression Using Burstsort and Elias Omega Coding

SRComp: Short Read Sequence Compression Using Burstsort and Elias Omega Coding | Computational Genomics | Scoop.it
“ by Jeremy John Selva, Xin Chen Next-generation sequencing (NGS) technologies permit the rapid production of vast amounts of data at low cost.”
Via Mel Melendrez-Vallard
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Rescooped by RickLStevens from Embedded Systems News
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Hardkernel Unveils $59 ODROID-U3 Board Powered by Exynos 4412 Prime Quad Core SoC

Hardkernel Unveils $59 ODROID-U3 Board Powered by Exynos 4412 Prime Quad Core SoC | Computational Genomics | Scoop.it
“ Hardkernel ODROID board family already features of the most cost effective development / honnyist boards in the market. But the company has done it again, with ODROID-U3 a quad core board, software...”
Via cnxsoft
RickLStevens's insight:
Awesome board. Need to compare to beagle hoard black.
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Rescooped by RickLStevens from Bioinformatics Software: Sequence Analysis
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kSNP v2 - Alignment-Free SNP Discovery and Phylogenetics of Hundreds of Microbial Genomes - Homologus Blog Post

kSNP v2 - Alignment-Free SNP Discovery and Phylogenetics of Hundreds of Microbial Genomes - Homologus Blog Post | Computational Genomics | Scoop.it
“ [...]”
Via Mel Melendrez-Vallard
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Nota other great use if k-mers
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Rescooped by RickLStevens from Bioinformatics Software: Sequence Analysis
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PLOS ONE: CNVannotator: A Comprehensive Annotation Server for Copy Number Variation in the Human Genome

PLOS ONE: CNVannotator: A Comprehensive Annotation Server for Copy Number Variation in the Human Genome | Computational Genomics | Scoop.it
“ PLOS ONE: an inclusive, peer-reviewed, open-access resource from the PUBLIC LIBRARY OF SCIENCE. Reports of well-performed scientific studies from all disciplines freely available to the whole world.”
Via Mel Melendrez-Vallard
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Rescooped by RickLStevens from Bioinformatics Software: Sequence Analysis
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On the simultaneous association analysis of large genomic regions: a massive multi-locus association test


Via Mel Melendrez-Vallard
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Rescooped by RickLStevens from Bioinformatics Software: Sequence Analysis
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Accurate detection of de novo and transmitted INDELs within exome-capture data using micro-assembly

Accurate detection of de novo and transmitted INDELs within exome-capture data using micro-assembly | Computational Genomics | Scoop.it

Via Mel Melendrez-Vallard
RickLStevens's insight:
I wonder how this compares to GATK and soap indel on human exome.
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Rescooped by RickLStevens from Bioinformatics Software: Sequence Analysis
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BMC Bioinformatics | Full text | Processing genome scale tabular data with wormtable

“ Modern biological science generates a vast amount of data, the analysis of which presents a major challenge to researchers.”
Via Mel Melendrez-Vallard
RickLStevens's insight:
I'm interested in putting support for things like this into hardware.
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