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chhylp123
2020-04-12 20:51:18 -04:00
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@@ -66,14 +66,12 @@ For Hifi reads assembly, a typical command line looks like:
``` ```
where `NA12878.fq.gz` is the input reads and `-o` specifies the output files. where `NA12878.fq.gz` is the input reads and `-o` specifies the output files.
In this example, all output files can be found at `NA12878.asm.*`. `-k`, `-t` In this example, all output files can be found at `NA12878.asm.*`. `-t` specifies
and `-r` specify the length of k-mer, the number of CPU threads, and the number the number of CPU threads. Note that at first run, hifiasm will save all overlaps
of correction rounds, respectively. Note that at first run, hifiasm will save to disk, which can avoid the time-consuming all-to-all overlap calculation next time.
all overlaps to disk, which can avoid the time-consuming all-to-all overlap For hifiasm, once the overlap information has been obtained during the previous run
calculation next time. For hifiasm, once the overlap information has been in advance, it is able to load all overlaps from disk and then directly do assembly.
obtained during the previous run in advance, it is able to load all overlaps If you want to ignore the pre-computed overlap information, please specify `-i`.
from disk and then directly do assembly. If you want to ignore the pre-computed
overlap information, please specify `-i`.
Please note that some old Hifi reads may consist of short adapters. To improve Please note that some old Hifi reads may consist of short adapters. To improve
the assembly quality, adapters should be removed by `-z` as follow: the assembly quality, adapters should be removed by `-z` as follow: