From 519d5b1eb18ed2427fcb6e358a91d3adf6ae0250 Mon Sep 17 00:00:00 2001 From: Heng Li Date: Sun, 4 Oct 2020 23:00:27 -0400 Subject: [PATCH 1/3] Updated the download link --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index cd34d7e..d121460 100644 --- a/README.md +++ b/README.md @@ -147,9 +147,9 @@ redwood genome in a few days on a single machine. For trio binning assembly: Except NA12878, the assemblies above were produced by hifiasm v0.7 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/v0.12/ ``` -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/ ``` From 00128c307609e34f6ebcbc806706458cbd30c38b Mon Sep 17 00:00:00 2001 From: Heng Li Date: Sun, 4 Oct 2020 23:01:16 -0400 Subject: [PATCH 2/3] Fixed the wrong download link --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index d121460..eb1ff54 100644 --- a/README.md +++ b/README.md @@ -144,10 +144,10 @@ 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/v0.12/ +ftp://ftp.dfci.harvard.edu/pub/hli/hifiasm/submission/hifiasm-0.12/ ``` NA12878 was assembled with an older version of hifiasm and is available at ```txt From 8cb131dca379442c0f4a927cac114fc2cb9c67b3 Mon Sep 17 00:00:00 2001 From: Heng Li Date: Mon, 5 Oct 2020 01:01:58 -0400 Subject: [PATCH 3/3] added a "Why hifiasm?" section --- README.md | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/README.md b/README.md index eb1ff54..d7ab9f2 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: