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update readme [skip ci] #46

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Oct 25, 2023
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update readme [skip ci] #46

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8 changes: 6 additions & 2 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -21,8 +21,12 @@ conda create -n dnaapler_env dnaapler
# activates conda environment
conda activate dnaapler_env

# runs dnaapler all
dnaapler all -i input_mixed_contigs.fasta -o output_directory_path -p my_bacteria_name -t 8

# runs dnaapler chromosome
dnaapler chromosome -i input.fasta -o output_directory_path -p my_bacteria_name -t 8
dnaapler chromosome -i input_chromosome.fasta -o output_directory_path -p my_bacteria_name -t 8

```

## Table of Contents
Expand Down Expand Up @@ -55,7 +59,7 @@ For bacterial chromosomes, `dnaapler chromosome` should ensure the chromosome br

Additionally, you can also reorient multiple bacterial chromosomes/plasmids/phages at once using the `dnaapler bulk` subcommand.

If your input FASTA is mixed (e.g. has chromosome and plasmids), you can also use `dnaapler all`, with the option to ignore some contigs with the `--ignore` parameter.
If your input FASTA is mixed (e.g. has chromosome and plasmids), you can also use `dnaapler all`, with the option to ignore some contigs with the `--ignore` parameter.

## Documentation

Expand Down