Results for "short"

Tags

  • PureCN: copy number calling and SNV classification using targeted short read sequencing

    This package estimates tumor purity, copy number, and loss of heterozygosity (LOH), and classifies single nucleotide variants (SNVs) by somatic status and clonality. PureCN is designed for targeted short read sequencing data, integrates well with standard somatic variant detection and copy number...

    Tags: PureCN, copy, number, calling, SNV, classification, targeted, short, read, sequencing

    2111 days ago

  • CoLoRMap: Correcting Long Reads by Mapping short reads

    Second generation sequencing technologies paved the way to an exceptional increase in the number of sequenced genomes, both prokaryotic and eukaryotic. However, short reads are difficult to assemble and often lead to highly fragmented assemblies. The recent developments in long reads sequencing m...

    Tags: CoLoRMap, Correcting, Long, Reads, Mapping, short, reads, pacbio

    2100 days ago

  • Rainbow: an integrated tool for efficient clustering and assembling RAD-seq reads

    Rainbow is developed to provide an ultra-fast and memory-efficient solution to clustering and assembling short reads produced by RAD-seq. First, Rainbow clusters reads using a spaced seed method. Then, Rainbow implements a heterozygote calling like strategy to divide potential groups into haploty...

    Tags: Rainbow, ultra-fast, memory-efficient, solution, clustering, assembling, short, reads, RAD-seq

    2040 days ago

  • Genome assembly tutorial "Genome Assembly for short and long reads"

    In this lab we will perform de novo genome assembly of a bacterial genome. You will be guided through the genome assembly starting with data quality control, through to building contigs and analysis of the results. At the end of the lab you will know: How to perform basic quality checks on the...

    Tags: Genome, assembly, tutorial, short, long, reads

    1948 days ago

  • vt: a variant tool set that discovers short variants from Next Generation Sequencing data.

    vt is a variant tool set that discovers short variants from Next Generation Sequencing data. https://genome.sph.umich.edu/wiki/Vt https://github.com/atks/vt

    Tags: vt, variant, tool, discovers, short, variants, Next, Generation, Sequencing, data

    1574 days ago

  • QuasR: Quantification and annotation of short reads in R

    The QuasR package (short for Quantify and annotate short reads in R) integrates the functionality of several R packages (such as IRanges (Lawrence et al. 2013) and Rsamtools) and external software (e.g. bowtie, through the Rbowtie package, and HISAT2, through the Rhisat2 package). The packag...

    Tags: QuasR, Quantification, annotation, short, reads, R, Tool, Reads

    1011 days ago