Control bowtie-build

[MeHelmy]

Hi,

It is written that:

• bowtie-build main function. It is placed in a separate source file
  • to make it slightly easier to compile as a library.
  • If the user specifies -A as the first two arguments, main
  • will interpret that file as having one set of command-line arguments
  • per line, and will dispatch each batch of arguments one at a time to
  • bowtie-build.

Is there any example how can I use -Aoption and example for the input parameter .

Thanks, Medhat

[mourisl]

This is to build several independent index. You need to use -A option by calling centrifuge-build-bin. The input parameter for -A is a file, where in this file, each line is a set of parameters used for centrifuge-build. For example, the file can be like:

--name-table centrifuge_name.out --conversion-table centrifuge_conversion.out --taxonomy-tree centrifuge_tax.out centrifuge_ref.fa test`
--name-table centrifuge_name2.out --conversion-table centrifuge_conversion2.out --taxonomy-tree centrifuge_tax2.out centrifuge_ref2.fa test2

And after calling "centrifuge-build-bin -A file_name" you will get two indices test.*.cf and test2.*.cf

[MeHelmy]

Thanks a lot for the answer.