diff --git a/README.md b/README.md index 4a5fd52..806dcf9 100644 --- a/README.md +++ b/README.md @@ -31,10 +31,10 @@ ViralMSA can be used as follows: usage: ViralMSA.py [-h] -s SEQUENCES -r REFERENCE -e EMAIL -o OUTPUT [-a ALIGNER] [-t THREADS] [-l] [--omit_ref] [--viralmsa_dir VIRALMSA_DIR] -h, --help show this help message and exit - -s SEQUENCES, --sequences SEQUENCES Input Sequences (FASTA format) (default: None) - -r REFERENCE, --reference REFERENCE Reference (default: None) - -e EMAIL, --email EMAIL Email Address (for Entrez) (default: None) - -o OUTPUT, --output OUTPUT Output Directory (default: None) + -s SEQUENCES, --sequences SEQUENCES Input Sequences (FASTA format) + -r REFERENCE, --reference REFERENCE Reference + -e EMAIL, --email EMAIL Email Address (for Entrez) + -o OUTPUT, --output OUTPUT Output Directory -a ALIGNER, --aligner ALIGNER Aligner (default: Minimap2) -t THREADS, --threads THREADS Number of Threads (default: max) -b BUFFER_SIZE, --buffer_size BUFFER_SIZE File Stream Buffer Size (bytes) (default: 1048576)