diff --git a/README.md b/README.md index a0fbdd7..4439a3e 100644 --- a/README.md +++ b/README.md @@ -31,7 +31,8 @@ adrsm -d ./data/genomes ./data/short_genome_list.csv ``` maxime@gph:~$ adrsm --help usage: ADRSM [-h] [-d DIRECTORY] [-r READLENGTH] [-l LENSTDEV] [-fwd FWDADAPT] - [-rev REVADAPT] [-e ERROR] [-o OUTPUT] [-q QUALITY] [-s STATS] + [-rev REVADAPT] [-e ERROR] [-p GEOM_P] [-m MIN] [-M MAX] + [-o OUTPUT] [-q QUALITY] [-s STATS] confFile Ancient DNA Read Simulator for Metagenomics @@ -49,10 +50,13 @@ optional arguments: -rev REVADAPT Reverse adaptor. Default = AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT -e ERROR Illumina sequecing error. Default = 0.01 + -p GEOM_P Geometric distribution parameter for deamination. Default = + 0.5 + -m MIN Deamination substitution base frequency. Default = 0.001 + -M MAX Deamination substitution max frequency. Default = 0.3 -o OUTPUT Output file basename. Default = ./metagenome.* -q QUALITY Base quality encoding. Default = d (PHRED+64) -s STATS Statistic file. Default = stats.csv - ``` ## Genome directory