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Showing 1 to 5 of 5 for “"SAMtools"”.
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Hardware acceleration of the SAMtools variant caller
… for a hardware-accelerated implementation of the SAMtools variant caller on an FPGA. It also includes a performance analysis of the algorithm and a proposed change to its software architecture to improve performance. SAMtools is normally invoked as a two-step command, where the results of samtools …
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Cancer risk prediction with next generation sequencing data using machine learning
… (INDEL) are identified and are filtered using SAMtools as well as with Genome Analyzer Tool Kit (GATK). Subsequently, the variants are encoded and feature selection is performed with the Pearson correlation coefficient (PCC) and the chi-square 2-df statistical test. Finally, 90:10 cross …
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Análisis de variabilidad de secuencia in vivo de RNAs circulares con ribozimas
… que se utilizan Biopython, bwa-mem, BCFtools y SAMtools, mientras que las estructuras secundarias se obtuvieron mediante el servicio web RNAalifold. En los experimentos realizados se confirmó la aparición de un mismo grupo de variantes estables que indicarían algún tipo de ventaja adaptativa o …
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Next-generation sequencing analysis and RNA editing in human brain and glioma
… any need for external software packages such as SAMtools (Heng Li et al. 2009). Quality filtering of input reads is incorporated directly into the alignment process. SNAP-RNA can automatically identify and report contaminants or viral/bacterial infections in samples, and gene read counts suitable …
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The chromatin landscape of colorectal cancer cells
… The mapped reads are then processed using samtools and duplicate reads are marked with the picard markduplicates argument. Narrow peaks are then called from processed reads using MACS2 and processed using bedtools. Called peaks then undergo a final quality control step using ChIPQCr and are …