diff --git a/README.md b/README.md index b541d70..2256fa5 100644 --- a/README.md +++ b/README.md @@ -118,7 +118,9 @@ mess run -i samples.tsv ``` > [!IMPORTANT] -> [Apptainer](https://apptainer.org/) is the default and recommended dependency deployment method for maximum reproducibility ! If you would like to use conda you can specify `--sdm conda`. +> [Apptainer](https://apptainer.org/) is the default and recommended dependency deployment method for maximum reproducibility ! +> +> If you would like to use conda you can specify `--sdm conda`. #### :card_index_dividers: Outputs @@ -197,7 +199,7 @@ seqkit stats --all -T -b mess_out/nanopore/fastq/* | :---------- | :------- | :------- | :------ | :---- | :----- | :----- | :------ | | phage.fq.gz | 1486 | 13203006 | 8884.9 | 12329 | 73.99 | 62.65 | 13.60 | -- PacBio +- PacBio HiFi ```sh mess run -i phage.tsv -o mess_out/pacbio --tech pacbio --error hifi @@ -212,6 +214,9 @@ seqkit stats --all -T -b mess_out/pacbio/fastq/* Inspired by [readSimulator](https://github.com/wanyuac/readSimulator)'s approach, `mess` can shuffle genome start points to get circular genome assemblies. +> [!WARNING] +> All contigs in the fasta will be circularised + - Linear (default, `--rotate 1`) ```sh @@ -232,6 +237,8 @@ mess run -i phage.tsv --rotate 3 -o mess_out/circular

+ +> [!NOTE] > Assembled using [unicycler](https://github.com/rrwick/Unicycler), visualized using [bandage](https://github.com/rrwick/Bandage) ## :sos: Help