Merge pull request #20 from rki-mf1/dev

Update README

README.md

@@ -13,12 +13,25 @@
 
 ## Requirements
 
-TL;DR: no external requirements needed if you are using the pre-build binary.
+TL;DR: no external requirements needed. Both the recursive GitHub clone as well as the bioconda package should work out-of-the-box.
 <details><summary> 🛠️ Details to build from source </summary>
 The <i>amplisim</i> software is intended for 64-bit POSIX compliant operating systems and was tested successfully under Ubuntu 22.04 LTS and macOS v12.5.1 (Monterey).
-Building <i>amplisim</i> from source requires libraries for <i>lzma</i>, <i>libbz2</i> and <i>libcurl</i> on your system in order to compile <i>htslib</i>.</details>
+Building <i>amplisim</i> from source requires libraries for <i>lzma</i>, <i>libbz2</i> and <i>libcurl</i> on your system in order to compile <i>htslib</i>.
+Both Linux and masOS operating systems typically provide them via their respective package managers. See intructions below.
+</details>
 
 ## Installation
+### Build via conda
+The easiest way to install _amplisim_ is via the conda package manager from the bioconda channel.
+Please note that the conda installation is currently only available for Linux operating systems.
+
+```
+# create a new conda environment
+conda create --name amplisim
+# install the latest amplisim version from the bioconda channel
+conda install -c bioconda amplisim
+```
+
 ### Build from source
 ```
 git clone --recursive https://github.com/Krannich479/amplisim.git
@@ -44,7 +57,7 @@ wget https://raw.githubusercontent.com/artic-network/primer-schemes/master/nCoV-
 wget https://www.ebi.ac.uk/ena/browser/api/fasta/MN908947.3
 sed 's/>ENA|MN908947|MN908947.3 Severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1, complete genome./>MN908947.3/g' MN908947.3 > MN908947.3.fasta
 cd ..
-./amplisim testdata/MN908947.3.fasta testdata/SARS-CoV-2.primer.bed
+amplisim testdata/MN908947.3.fasta testdata/SARS-CoV-2.primer.bed
 ```
 
 ## Operation
@@ -55,8 +68,12 @@ The most concise way to get familiar with _amplisim_ is to inspect the help page
 Usage: amplisim [OPTION...] REFERENCE PRIMERS
 amplisim -- a program to simulate amplicon sequences from a reference genome
 
+  -m, --mean=INT             Set the mean number of replicates per amplicon
+  -n, --sd=INT               Set the standard deviation for the mean number of
+                             replicates per amplicon
   -o, --output=FILE          Output to FILE instead of standard output
   -s, --seed=INT             Set a random seed
+  -x, --dropout=INT          Set the likelihood for an amplicon dropout [0,1]
   -?, --help                 Give this help list
       --usage                Give a short usage message
   -V, --version              Print program version
@@ -69,11 +86,11 @@ Report bugs to https://github.com/rki-mf1/amplisim/issues.
 
 ### Minimal working examples
 The minimal command to run _amplisim_ is to provide a reference genome in FASTA format and a set of primers in BED format (see chapter [Input and output](#input-and-output) for more details).
-By default, _amplisim_ prints the amplicons sequences to the standard output, s.t. the user can either store the sequences or forward them to the next program.
+By default, _amplisim_ prints the amplicons sequences to the standard output such that the user can either direct the sequences to a file or forward them to the next program.
 ```
 amplisim <my_reference.fasta> <my_primers.bed> > <my_amplicons.fasta>
 ```
-If you are just interested in the resulting FASTA file you can directly use the `-o` option.
+If you want _amplisim_ to store the resulting amplicon sequences directly in a FASTA file you can use the `-o` option.
 ```
 amplisim -o <my_amplicons.fasta> <my_reference.fasta> <my_primers.bed>
 ```