bioinformatics tools
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PhenoMan: phenotypic data exploration, selection, management and quality control for association studies of rare and common variants

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PLOS ONE: Fast Identification and Removal of Sequence Contamination from Genomic and Metagenomic Datasets

PLOS ONE: Fast Identification and Removal of Sequence Contamination from Genomic and Metagenomic Datasets | bioinformatics tools | 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.
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Specificity control for read alignments using an artificial reference genome-guided false discovery rate

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MATE-CLEVER: Mendelian-inheritance-aware discovery and genotyping of midsize and long indels

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BlastGraph: a comparative genomics tool based on BLAST and graph algorithms

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PLOS ONE: RNA-CODE: A Noncoding RNA Classification Tool for Short Reads in NGS Data Lacking Reference Genomes

PLOS ONE: RNA-CODE: A Noncoding RNA Classification Tool for Short Reads in NGS Data Lacking Reference Genomes | bioinformatics tools | Scoop.it
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NextGenMap: fast and accurate read mapping in highly polymorphic genomes

Summary: When choosing a read mapper, one faces the trade off between speed and the ability to map reads in highly polymorphic regions. Here, we report NextGenMap, a fast and accurate read mapper, which reduces this dilemma. NextGenMap aligns reads reliably to a reference genome even when the sequence difference between target and reference genome is large, i.e. highly polymorphic genome. At the same time, NextGenMap outperforms current mapping methods with respect to runtime and to the number of correctly mapped reads.NextGenMap efficiently uses the available hardware by exploiting multi-core CPUs as well as graphic cards (GPUs), if available. In addition,NextGenMap handles automatically any read data independent of read length and sequencing technology.

 
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SW#–GPU-enabled exact alignments on genome scale

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Summary: We propose SW#, a new CUDA graphical processor unit-enabled and memory-efficient implementation of dynamic programming algorithm, for local alignment. It can be used as either a stand-alone application or a library. Although there are other graphical processor unit implementations of the Smith–Waterman algorithm, SW# is the only one publicly available that can produce sequence alignments on genome-wide scale. For long sequences, it is at least a few hundred times faster than a CPU version of the same algorithm

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SPANNER: taxonomic assignment of sequences using pyramid matching of similarity profiles

SPANNER: taxonomic assignment of sequences using pyramid matching of similarity profiles | bioinformatics tools | Scoop.it
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Microbial Informatics and Experimentation | Full text | An efficient rRNA removal method for RNA sequencing in GC-rich bacteria

Microbial Informatics and Experimentation | Full text | An efficient rRNA removal method for RNA sequencing in GC-rich bacteria | bioinformatics tools | Scoop.it
Next generation sequencing (NGS) technologies have revolutionized gene expression studies and functional genomics analysis.
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A poor man’s BLASTX—high-throughput metagenomic protein database search using PAUDA

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STAR: an integrated solution to management and visualization of sequencing data

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PLOS ONE: Generation of Physical Map Contig-Specific Sequences Useful for Whole Genome Sequence Scaffolding

PLOS ONE: Generation of Physical Map Contig-Specific Sequences Useful for Whole Genome Sequence Scaffolding | bioinformatics tools | Scoop.it
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ACCUSA2: multi-purpose SNV calling enhanced by probabilistic integration of quality scores

ACCUSA2: multi-purpose SNV calling enhanced by probabilistic integration of quality scores | bioinformatics tools | Scoop.it
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ReviSTER: an automated pipeline to revise misaligned reads to simple tandem repeats

ReviSTER: an automated pipeline to revise misaligned reads to simple tandem repeats | bioinformatics tools | Scoop.it
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SPOCS: software for predicting and visualizing orthology/paralogy relationships among genomes

SPOCS: software for predicting and visualizing orthology/paralogy relationships among genomes | bioinformatics tools | Scoop.it
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