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Haoyu Cheng
2019-12-26 17:08:37 -05:00
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README.md
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@@ -33,7 +33,7 @@ For Hifi reads assembly, a typical command line looks like:
where `-q` specifies the input reads and `-o` specifies the output files. In this example, the assembly graph can be found at NA12878.asm.fa.gfa, and the corrected reads can be found at NA12878.asm.fa. `-k`, `-t` and `-r` specify the length of k-mer, the number of CPU threads, and the number of correction rounds, respectively. Note that `-w` means hifiasm will save all overlaps to disk, which can avoid the time-consuming all-to-all overlap calculation next time. For hifiasm with `-l`, if the overlap information has been obtained by `-w` in advance, it is able to load all overlaps from disk and then directly do assembly.
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:
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:
```sh
./hifiasm -w -l -q butterfly.fq.gz -o butterfly_asm_clean.fa -k 40 -t 42 -r 2 -z 20