diff --git a/README.md b/README.md index cd34d7e..ac76766 100644 --- a/README.md +++ b/README.md @@ -30,6 +30,29 @@ produce primary/alternate assemblies of quality competitive with the best assemblers. It also introduces a new graph binning algorithm and achieves the best haplotype-resolved assembly given trio data. +## Why Hifiasm? + +* Hifiasm delivers high-quality assemblies. It tends to generate longer contigs + and resolve more segmental duplications than other assemblers. + +* Given sequence reads from the parents, hifiasm can produce overall the best + haplotype-resolved assembly so far. It is the assembler of choice by the + [Human Pangenome Project][hpp] for the first batch of samples. + +* Hifiasm can purge duplications between haplotigs without relying on + third-party tools such as purge\_dups. Hifiasm does not need polishing tools + like pilon or racon, either. This simplifies the assembly pipeline and saves + running time. + +* Hifiasm is fast. It can assemble a human genome in half a day and assemble a + ~30Gb redwood genome in three days. No genome is too large for hifiasm. + +* Hifiasm is trivial to install and easy to use. It does not required python, + R or C++11 compilers and can be compiled into a single executable. The + default setting works well with a variety of genomes. + +[hpp]: https://humanpangenome.org + ## Usage A typical hifiasm command line looks like: @@ -144,12 +167,12 @@ redwood genome in a few days on a single machine. For trio binning assembly: [NA12891-data]: https://www.ebi.ac.uk/ena/data/view/ERR194160 [NA12892-data]: https://www.ebi.ac.uk/ena/data/view/ERR194161 -Except NA12878, the assemblies above were produced by hifiasm v0.7 and can be +Except NA12878, the assemblies above were produced by hifiasm v0.12 and can be downloaded at ```txt -ftp://ftp.dfci.harvard.edu/pub/hli/hifiasm/submission/v0.7/ +ftp://ftp.dfci.harvard.edu/pub/hli/hifiasm/submission/hifiasm-0.12/ ``` -NA12878 was assembled with a more recent version of hifiasm and is available at +NA12878 was assembled with an older version of hifiasm and is available at ```txt ftp://ftp.dfci.harvard.edu/pub/hli/hifiasm/NA12878-r253/ ``` @@ -169,4 +192,4 @@ page](https://github.com/chhylp123/hifiasm/issues). ## Limitations -1. Purging haplotig duplications may introduce misassemblies. +1. Purging haplotig duplications may introduce misassemblies. \ No newline at end of file