From 9ef00f749a940fe60edf9dc8534e31a02d999071 Mon Sep 17 00:00:00 2001 From: Haoyu Cheng Date: Thu, 26 Dec 2019 14:44:11 -0500 Subject: [PATCH] update README --- CommandLines.cpp | 2 +- README.md | 9 ++++++--- 2 files changed, 7 insertions(+), 4 deletions(-) diff --git a/CommandLines.cpp b/CommandLines.cpp index 1640a3e..361e2f4 100644 --- a/CommandLines.cpp +++ b/CommandLines.cpp @@ -33,7 +33,7 @@ void Print_H(hifiasm_opt_t* asm_opt) fprintf(stderr, " -y FLOAT min overlap drop ratio [%.2g]\n", asm_opt->min_drop_rate); fprintf(stderr, " -v show version number\n"); fprintf(stderr, " -h show help information\n"); - fprintf(stderr, "Example: ./hifiasm -w -l -q NA12878.fq.gz -o NA12878.asm -k 40 -t 32 -r 2 -a 4 -z 0\n"); + fprintf(stderr, "Example: ./hifiasm -w -l -q NA12878.fq.gz -o NA12878.asm -k 40 -t 32 -r 2\n"); } diff --git a/README.md b/README.md index e0f745e..2e8052c 100644 --- a/README.md +++ b/README.md @@ -1,9 +1,12 @@ ## Getting Started ```sh -# Install hifiasm and miniasm (requiring g++ and zlib) +# Install hifiasm (requiring g++ and zlib) git clone https://github.com/chhylp123/hifiasm.git cd hifiasm && make # Assembly (corrected reads are at NA12878.asm.fa, assembly graph is at NA12878.asm.fa.gfa) -./hifiasm -w -l -q NA12878.fq.gz -o NA12878.asm.fa -k 40 -t 32 -r 2 -a 4 -z 0 -``` \ No newline at end of file +./hifiasm -w -l -q NA12878.fq.gz -o NA12878.asm.fa -k 40 -t 32 -r 2 +``` + +## Introduction +Hifiasm is an ultrafast haplotype-resolved de novo assembler based on PacBio Hifi reads. Unlike most existing assemblers, hifiasm starts from uncollapsed genome. Thus, it is able to keep the haplotype information as much as possible. The input of hifiasm is the PacBio Hifi reads in fasta/fastq format, and there are two types of output: (1) haplotype-resolved assembly graph in GFA format; (2) Haplotype-aware error corrected reads. So far Hifiasm is in early development stage, it will support phased chromosome-level high-quality assembly in the near future. \ No newline at end of file