diff --git a/README.md b/README.md index a617c575..d96f3c8b 100644 --- a/README.md +++ b/README.md @@ -69,7 +69,7 @@ python src/concatenate.py /path/to/catalogue.fna.gz /path/to/assemblies/sample1/ 3. Use your favorite short-read aligner to map each your read files back to the resulting FASTA file: ``` -minimap2 -I 50G -d catalogue.mmi /path/to/catalogue.fna.gz; # make index +minimap2 -d catalogue.mmi /path/to/catalogue.fna.gz; # make index minimap2 -t 8 -N 50 -ax sr catalogue.mmi /path/to/reads/sample1.fw.fq.gz /path/to/reads/sample1.rv.fq.gz | samtools view -F 3584 -b --threads 8 > /path/to/bam/sample1.bam ```