Add badges, update Readme and modify it in markdown

README.org → README.md

@@ -1,15 +1,21 @@
-* proovframe: frame-shift correction for long read (meta)genomics
+[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/proovframe/README.html)
+[![Anaconda-Server Badge](https://img.shields.io/conda/dn/bioconda/proovframe.svg?style=flat)](https://anaconda.org/bioconda/proovframe)
+[![DOI](https://img.shields.io/badge/DOI-10.1101/2021.08.23.457338-blue)](https://doi.org/10.1101/2021.08.23.457338)
+[![Anaconda-Server Badge](https://anaconda.org/bioconda/proovframe/badges/license.svg)](https://anaconda.org/bioconda/proovframe)
+
+
+proovframe: frame-shift correction for long read (meta)genomics
+=========================================
 
 Gene prediction on long reads, aka PacBio and Nanopore, is often impaired by
 indels causing frameshift. Proovframe detects and corrects frameshifts in coding
 sequences from raw long reads or long-read derived assemblies.  
 
-#+ATTR_HTML: :width 600px
-[[file:implementation.png]]
+<img src="implementation.png" width="1000px" height="600px" />
 
 Proovframe uses frameshift-aware alignments to reference proteins as guides, and
 conservatively restores frame-fidelity by 1/2-base deletions or insertions of
-"N/NN"s, and masking of premature stops ("NNN").
+`N/NN`s, and masking of premature stops (`NNN`).
 
 Good results can already be obtained with distantly related guide proteins-
 successfully tested with sets with <60% amino acid identity.
@@ -20,22 +26,40 @@ consensus-polishing approaches for assemblies.
 It can be used on raw reads directly, which means it can be used on data lacking
 sequencing depth for consensus polishing - a common problem for a lot of rare
 things from environmental metagenomic samples, for example.
-
 
-** Usage
+## Install 
+
+### bioconda
 
-Requires  [[https://github.com/bbuchfink/diamond][DIAMOND v2.0.3]] or newer for mapping.
+```
+conda install -c bioconda proovframe
+```
 
-#+begin_src sh
-# install
+### Manual
+
+Requires  [DIAMOND v2.0.3](https://github.com/bbuchfink/diamond) or newer for mapping.
+
+```
 git clone https://github.com/thackl/proovframe
-# map proteins to reads
+```
+
+It is ready to be used. The tool lives in `proovframe/bin/proovframe`
+
+
+## Usage
+
+map proteins to reads: 
+``` 
 proovframe/bin/proovframe map -a proteins.faa -o raw-seqs.tsv raw-seqs.fa
-# fix frameshifts in reads
+```
+
+fix frameshifts in reads:
+```
 proovframe/bin/proovframe fix -o corrected-seqs.fa raw-seqs.fa raw-seqs.tsv
-#+end_src
+```
+
 
-** Citing
+## Citing
 
 If you use proovframe and DIAMOND please cite: