Update README.md

README.md

@@ -1,18 +1,18 @@
 # shiver
 Sequences from HIV Easily Reconstructed.  
 
-<p align="center"><img src="info/AssemblyPipelineDiagram_ForPaper.png" width=800, height="370"/></p>
+<p align="center"><img src="docs/AssemblyPipelineDiagram_ForPaper.png" width=800, height="370"/></p>
 
 shiver is freely available under the GNU General Public License version 3, described [here](LICENSE).  
 shiver is a tool for mapping reads (fragments of genetic sequence) to a custom reference sequence constructed using _de novo_ assembled contigs, in order to minimise the biased loss of information that occurs from mapping to a 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](https://doi.org/10.1093/ve/vey007); please cite this if you find shiver, or our discussion of the relevant issues, helpful.
-If you use shiver, please also cite its dependencies. Citation details [here](info/CitationDetails.bib).
+If you use shiver, please also cite its dependencies. Citation details [here](docs/CitationDetails.bib).
 
 shiver runs natively on Linux and Mac OS, but not Windows.
 However on any operating system (including Windows), if you have [VirtualBox](https://www.virtualbox.org/wiki/Downloads) installed, you can run [this](https://drive.google.com/file/d/1MohIOgJxcFVRv9v0aG2vyvEVgtm8lcyc/view?usp=sharing) image of Ubuntu Linux 22.04 which contains shiver and our separate tool [phyloscanner](https://github.com/BDI-pathogens/phyloscanner) (which allows you to investigate the within- and between-host diversity in mapped reads produced e.g. by shiver).
 Instructions for the image (and full steps for how everything was installed) are [here](https://docs.google.com/document/d/1tX1juaiBhEZ5aW740ME05zaMm480Aj1eFvyY-H3Aor8/edit?usp=sharing).  
 shiver dependencies: [samtools](http://www.htslib.org/), [biopython](http://biopython.org/wiki/Download), [mafft](http://mafft.cbrc.jp/alignment/software/), [blast](https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download) version 2.2.28 or higher (warning: earlier versions of blast have a bug that prevents shiver from correcting contigs), [trimmomatic](http://www.usadellab.org/cms/?page=trimmomatic) (optional: needed if you want to trim reads for quality or adapter sequences), [Fastaq](https://github.com/sanger-pathogens/Fastaq) (optional: needed if you want to trim reads for primers), and at least one of [smalt](http://www.sanger.ac.uk/science/tools/smalt-0) or [BWA](http://bio-bwa.sourceforge.net/) or [bowtie](http://bowtie-bio.sourceforge.net/index.shtml) for mapping.
-Installation instructions for all of these are [here](info/InstallationNotes.sh).  
+Installation instructions for all of these are [here](docs/InstallationNotes.sh).  
 
-The shiver manual is [here](info/ShiverManual.pdf).
+The shiver manual is [here](docs/ShiverManual.pdf).