After you have finished running 2bwt_builder_cpu or 2bwt_builder_gpu, and AsiicBWT2BWT.
you will get files like:
prefix.*, including prefix.bwt, prefix.f.bwt.ascii...
Now you have already construct the 2bwt of reads.
To further run BASE,
You need to prepare a "2bwt_index" file to tell BASE the path to find the 2bwt.
in this file, you need to include bwts by line:
dir/prefix insert_size sd flag
dir: is the directory to keep prefix.
prefix: is the prefix used to build 2bwt.
insert_size: is the expected insert size of the pair end reads in bwt.
sd: is the standard diviation of the insert sizes.
flag: set whether reads in this bwt will be used to find initial seed(1) or not(0).
the four columns mentioned above are seperated by a blank " ".
Last edit: Binghang Liu 2016-11-21
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After you have finished running 2bwt_builder_cpu or 2bwt_builder_gpu, and AsiicBWT2BWT.
you will get files like:
prefix.*, including prefix.bwt, prefix.f.bwt.ascii...
Now you have already construct the 2bwt of reads.
To further run BASE,
You need to prepare a "2bwt_index" file to tell BASE the path to find the 2bwt.
in this file, you need to include bwts by line:
dir/prefix insert_size sd flag
dir: is the directory to keep prefix.
prefix: is the prefix used to build 2bwt.
insert_size: is the expected insert size of the pair end reads in bwt.
sd: is the standard diviation of the insert sizes.
flag: set whether reads in this bwt will be used to find initial seed(1) or not(0).
the four columns mentioned above are seperated by a blank " ".
Last edit: Binghang Liu 2016-11-21