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Tool name, like bwa, HISAT2 etc. If there is a subcommand involved, please include both the software (e.g. samtools) and the subcommand. For example, if you want to tell people how to generate index for bwa, please type bwa index in the textbox.

Short usage hints, like

bwa index [-p prefix] [-a algoType]


Index database sequences in the FASTA format.

Parameter list and usage examples of this tool, like


  • --region CHR:START:END, -r CHR:START:END: Region of the genome to limit the operation to - this is useful when testing parameters to reduce the computing time. The format is chr:start:end, for example --region chr10. (default: None)
If you want to refer to another tool, link the text to the corresponding webpage then style the text as Computer Code. If you want to refer to another option, style the text as Cited Option.

Link to the tool's documentation or DOI id of the paper.

A short alias for this record.

How to access the source code?

How to access the binary/executable files?

What category does it belong to?

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