Update README

README.md

@@ -13,7 +13,8 @@ cd hifiasm && make
 Hifiasm is a fast haplotype-resolved de novo assembler for 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 its
+
+For non-trio assembly, the input of hifiasm is the PacBio Hifi reads in fasta/fastq format, and its
 outputs consist of: 
 
 1. Haplotype-resolved raw [unitig][unitig] graph in [GFA][gfa] format
@@ -30,9 +31,18 @@ outputs consist of:
 5. Haplotype-aware error corrected reads in fasta format (*prefix*.ec.fa).
 6. All-to-all overlaps in the [PAF][paf] format (*prefix*.ovlp.paf).
 
-So far hifiasm is still in early development stage, it will output phased
-chromosome-level high-quality assembly in the near future. In addition, hifiasm
-also outputs three binary files that save all overlap inforamtion
+For trio assembly, the input of hifiasm is the PacBio Hifi reads in fasta/fastq format, and the paternal/maternal trio indexes generated by `yak count` (see https://github.com/lh3/yak). The outputs consist of:
+1. Haplotype-resolved raw [unitig][unitig] graph in [GFA][gfa] format
+   (*prefix*.r\_utg.gfa). This graph keeps all haplotype information. 
+
+2. Phased maternal unitig graph (*prefix*.m.r\_utg.gfa).
+This graph keeps the phased maternal assembly.
+
+3. Phased paternal unitig graph (*prefix*.p.r\_utg.gfa).
+This graph keeps the phased paternal assembly.
+
+
+In addition, hifiasm also outputs three binary files that save all overlap inforamtion
 (hifiasm.asm.ovlp, hifiasm.asm.ovlp.source, hifiasm.asm.ovlp.reverse in default). With these files, hifiasm can avoid the time-consuming all-to-all overlap calculation step, and do the assembly
 directly and quickly. This might be helpful when you want to get an optimized
 assembly by multiple rounds of experiments with different parameters.
@@ -44,7 +54,7 @@ assembly in a few hours. Hifiasm has been tested on the following datasets:
 |<sub>Dataset<sub>|<sub>GSize<sub>|<sub>Cov<sub>|<sub>Asm options<sub>|<sub>CPU time<sub>|<sub>Wall time<sub>|<sub>RAM<sub>|<sub>[unitig][unitig]/[contig][unitig] N50<sup>[1]</sup><sub>|
 |:---------------|-----:|-----:|:---------------------|-------:|--------:|----:|----------------:|
 |<sub>[Human NA12878]<sub>|<sub>3Gb<sub>|<sub>x28<sub>|<sub>-k 40 -t 42 -r 2<sub>|<sub>200h<sub>|    <sub>5h32m<sub>|<sub>114G<sub>|<sub>93.5Kb/28.2Mb<sub>|
-|<sub>[Human HG002]<sub>|<sub>3Gb<sub>|<sub>x43<sub>|<sub>-k 40 -t 42 -r 2<sub>|<sub>405h10m<sub>|<sub>12h7m<sub>|<sub>146G<sub>|<sub>320kb/35.3Mb<sub>|
+|<sub>[Human HG002]<sub>|<sub>3Gb<sub>|<sub>x43<sub>|<sub>-k 40 -t 42 -r 2<sub>|<sub>405h10m<sub>|<sub>12h7m<sub>|<sub>146G<sub>|<sub>320kb/46.0Mb<sub>|
 |<sub>[Human CHM13]<sub>|<sub>3Gb<sub>|<sub>x27<sub>|<sub>-k 40 -t 42 -r 2<sub>|<sub>157h28m<sub>|<sub>5h10m<sub>|<sub>85.8G<sub>|<sub>NA<sup>[2]</sup>/41.4Mb<sub>|
 |<sub>[Butterfly]<sub>|<sub>358Mb<sub>|<sub>x35<sub>|<sub>-k 40 -t 42 -r 2 -z 20<sub>|<sub>17h6m<sub>|<sub>36m<sub>|<sub>16G<sub>|<sub>7.5Mb/NA<sup>[3]</sup><sub>|
 
@@ -85,6 +95,22 @@ the assembly quality, adapters should be removed by `-z` as follow:
 
 In this example, hifiasm will remove 20 bases from both ends of each read.
 
+For trio assembly, first the trio indexes of paternal/maternal should be generated by 
+`yak count` (see https://github.com/lh3/yak):
+
+```sh
+./yak count -k31 -b37 -t16 -o mat.yak mat.fq.gz
+```
+```sh
+./yak count -k31 -b37 -t16 -o pat.yak pat.fq.gz
+```
+
+and then run hifiasm as follow:
+
+```sh
+./hifiasm -o NA12878.asm -t 32 -P pat.yak -M mat.yak NA12878_1.fq.gz NA12878_2.fq.gz
+```
+
 [unitig]: http://wgs-assembler.sourceforge.net/wiki/index.php/Celera_Assembler_Terminology
 [gfa]: https://github.com/pmelsted/GFA-spec/blob/master/GFA-spec.md
 [paf]: https://github.com/lh3/miniasm/blob/master/PAF.md

hifiasm.1

@@ -1,4 +1,4 @@
-.TH hifiasm 1 "3 Jan 2020" "hifiasm-0.3.0" "Bioinformatics tools"
+.TH hifiasm 1 "22 Mar 2020" "hifiasm-0.3.0" "Bioinformatics tools"
 
 .SH NAME
 .PP