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Sequences from HIV Easily Reconstructed
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README.md

shiver

Sequences from HIV Easily Reconstructed.

shiver is freely available under the GNU General Public License version 3, described here.
shiver is a tool for mapping paired-end short reads to a custom reference sequence constructed using do novo assembled contigs, in order to minimise the biased loss of information that occurs from mapping to an reference that differs from the sample. From the mapped reads, base frequencies are calculated, and a consensus sequence is called.
The method, its performance and scientific context are discussed here; please cite this if you find shiver helpful. If you use shiver, please also cite the publications of its dependencies. Citation details here.

shiver runs natively on Linux and Mac OS, but not Windows. However on any operating system (including Windows), if you have VirtualBox installed, you can run this image of Ubuntu Linux 16.04.3 which contains shiver, our separate tool phyloscanner (which allows you to investigate the within- and between-host diversity in mapped reads produced e.g. by shiver), all of their dependencies, and also the assembler SPAdes which can be used to assemble contigs suitable as input for shiver.
shiver dependencies: Fastaq, samtools, biopython, mafft, blast version 2.2.28 or higher (warning: earlier versions of blast have a bug that prevents shiver from correcting contigs), trimmomatic (optional: needed if you want to trim reads for quality or adapter sequences) and at least one of smalt or BWA or bowtie for mapping. Installation instructions for all of these are here.

The shiver manual is here.

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