From d72f9b9c3af67c93e03651d8357ee60e23ccbbf5 Mon Sep 17 00:00:00 2001 From: Haoyu Cheng Date: Thu, 26 Dec 2019 16:32:26 -0500 Subject: [PATCH] readme --- README.md | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/README.md b/README.md index 8bfb2ce..c35e01c 100644 --- a/README.md +++ b/README.md @@ -24,3 +24,11 @@ Hifiasm is a standalone and lightweight assembler, which does not need external [2] CHM13 is a homozygous sample, so unitig N50 makes no sense. [3] Butterfly has high heterozygous rate, so most chromosomes have been fully separated into two haplotypes. In this case, contig N50 makes no sense. +## Usage +For Hifi reads assembly, a typical command line looks like: + +```sh +./hifiasm -w -l -q NA12878.fq.gz -o NA12878.asm.fa -k 40 -t 32 -r 2 +``` +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. In this case, hifiasm with `-l` is able to load all overlaps from disk and then directly do assembly. +