diff --git a/README.md b/README.md index e36acc3..7e8a7b2 100644 --- a/README.md +++ b/README.md @@ -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. -In this example, all output files can be found at `NA12878.asm.*`. `-k`, `-t` -and `-r` specify the length of k-mer, the number of CPU threads, and the number -of correction rounds, respectively. Note that at first run, hifiasm will save -all overlaps to disk, which can avoid the time-consuming all-to-all overlap -calculation next time. For hifiasm, once the overlap information has been -obtained during the previous run in advance, it is able to load all overlaps -from disk and then directly do assembly. If you want to ignore the pre-computed -overlap information, please specify `-i`. +In this example, all output files can be found at `NA12878.asm.*`. `-t` specifies +the number of CPU threads. Note that at first run, hifiasm will save all overlaps +to disk, which can avoid the time-consuming all-to-all overlap calculation next time. +For hifiasm, once the overlap information has been obtained during the previous run +in advance, it is able to load all overlaps 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 the assembly quality, adapters should be removed by `-z` as follow: