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@@ -25,85 +25,9 @@ hifiasm -o HG002.asm -t32 -1 pat.yak -2 mat.yak HG002-HiFi.fa.gz
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.
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
(*prefix*.r\_utg.gfa). This graph keeps all haplotype information, including
somatic mutations and recurrent sequencing errors.
2. Haplotype-resolved processed unitig graph without small bubbles
(*prefix*.p\_utg.gfa). Small bubbles might be caused by somatic mutations or noise in data,
which are not the real haplotype information.
3. Primary assembly [contig][unitig] graph (*prefix*.p\_ctg.gfa). This graph collapses different
haplotypes.
4. Alternate assembly contig graph (*prefix*.a\_ctg.gfa). This graph consists of all assemblies that
are discarded in primary contig graph.
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](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 paternal/haplotype1 contig graph (*prefix*.hap1.p\_ctg.gfa). This graph keeps the phased
paternal/haplotype1 assembly.
3. Phased maternal/haplotype2 contig graph (*prefix*.hap2.p\_ctg.gfa). This graph keeps the phased
maternal/haplotype2 assembly.
Hifiasm supports both primary assembly and fully phased assembly (trio-binning assembly).
In addition, hifiasm also outputs three binary files that save all overlap information (*prefix*.ec.bin, *prefix*.ovlp.reverse.bin, *prefix*.ovlp.source.bin). 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.
Hifiasm is a standalone and lightweight assembler, which does not need external
libraries (except zlib). For large genomes, it can generate high-quality primary
assembly in several hours. Hifiasm has been tested on various large and complex datasets.
The results are as follows:
|<sub>Dataset<sub>|<sub>Size<sub>|<sub>Cov.<sub>|<sub>Asm options<sub>|<sub>CPU time<sub>|<sub>Wall time<sub>|<sub>RAM<sub>|<sub> N50<sub>|
|:---------------|-----:|-----:|:---------------------|-------:|--------:|----:|----------------:|
|<sub>[Mouse (C57/BL6J)][mouse-data]</sub>|<sub>2.6Gb</sub> |<sub>&times;25</sub>|<sub>-t48 -l0</sub> |<sub>172.9h</sub> |<sub>4.8h</sub> |<sub>76G</sub> |<sub>21.1Mb</sub>|
|<sub>[Maize (B73)][maize-data]</sub> |<sub>2.2Gb</sub> |<sub>&times;22</sub>|<sub>-t48 -l0</sub> |<sub>203.2h</sub> |<sub>5.1h</sub> |<sub>68G</sub> |<sub>36.7Mb</sub>|
|<sub>[Strawberry][strawberry-data]</sub> |<sub>0.8Gb</sub> |<sub>&times;36</sub>|<sub>-t48 -D10</sub>|<sub>152.7h</sub> |<sub>3.7h</sub> |<sub>91G</sub> |<sub>17.8Mb</sub>|
|<sub>[Frog][frog-data]</sub> |<sub>9.5Gb</sub> |<sub>&times;29</sub>|<sub>-t48</sub> |<sub>2834.3h</sub>|<sub>69.0h</sub>|<sub>463G</sub>|<sub>9.3Mb</sub>|
|<sub>[Redwood][redwood-data]</sub> |<sub>35.6Gb</sub>|<sub>&times;28</sub>|<sub>-t80</sub> |<sub>3890.3h</sub>|<sub>65.5h</sub>|<sub>699G</sub>|<sub>5.4Mb</sub>|
|<sub>[Human (CHM13)][CHM13-data]</sub> |<sub>3.1Gb</sub> |<sub>&times;32</sub>|<sub>-t48 -l0</sub> |<sub>310.7h</sub> |<sub>8.2h</sub> |<sub>114G</sub>|<sub>88.9Mb</sub>|
|<sub>[Human (HG00733)][HG00733-data]</sub>|<sub>3.1Gb</sub>|<sub>&times;33</sub>|<sub>-t48</sub> |<sub>269.1h</sub> |<sub>6.9h</sub> |<sub>135G</sub>|<sub>69.9Mb</sub>|
|<sub>[Human (HG002)][NA24385-data]</sub> |<sub>3.1Gb</sub> |<sub>&times;36</sub>|<sub>-t48</sub> |<sub>305.4h</sub> |<sub>7.7h</sub> |<sub>137G</sub>|<sub>98.7Mb</sub>|
[mouse-data]: https://www.ncbi.nlm.nih.gov/sra/?term=SRR11606870
[maize-data]: https://www.ncbi.nlm.nih.gov/sra/?term=SRR11606869
[strawberry-data]: https://www.ncbi.nlm.nih.gov/sra/?term=SRR11606867
[frog-data]: https://www.ncbi.nlm.nih.gov/sra?term=(SRR11606868)%20OR%20SRR12048570
[redwood-data]: https://www.ncbi.nlm.nih.gov/sra/?term=SRP251156
[CHM13-data]: https://www.ncbi.nlm.nih.gov/sra?term=(((SRR11292120)%20OR%20SRR11292121)%20OR%20SRR11292122)%20OR%20SRR11292123
Hifiasm also can produce high-quality fully resolved assembly. We tested it on the following trio-binning datasets:
|<sub>Dataset<sub>|<sub>Cov.<sub>|<sub>CPU time<sub>|<sub>Elapsed time<sub>|<sub>RAM<sub>|<sub> N50<sub>|
|:---------------|-----:|-------:|--------:|----:|----------------:|
|<sub>[HG00733][HG00733-data], [\[father\]][HG00731-data], [\[mother\]][HG00732-data]</sub>|<sub>&times;33</sub>|<sub>269.1h</sub>|<sub>6.9h</sub>|<sub>135G</sub>|<sub>35.1Mb (paternal), 34.9Mb (maternal)</sub>|
|<sub>[HG002][NA24385-data], [\[father\]][NA24149-data], [\[mother\]][NA24143-data]</sup>|<sub>&times;36</sub>|<sub>305.4h</sub>|<sub>7.7h</sub>|<sub>137G</sub>|<sub>41.0Mb (paternal), 40.8Mb (maternal)</sub>|
|<sub>[NA12878][NA12878-data], [\[father\]][NA12891-data], [\[mother\]][NA12892-data]</sub>|<sub>&times;30</sub>|<sub>180.8h</sub>|<sub>4.9h</sub>|<sub>123G</sub>|<sub>27.7Mb (paternal), 27.0Mb (maternal)</sub>|
[HG00733-data]: https://www.ebi.ac.uk/ena/data/view/ERX3831682
[HG00731-data]: https://www.ebi.ac.uk/ena/data/view/ERR3241754
[HG00732-data]: https://www.ebi.ac.uk/ena/data/view/ERR3241755
[NA24385-data]: https://www.ncbi.nlm.nih.gov/sra?term=(((SRR10382244)%20OR%20SRR10382245)%20OR%20SRR10382248)%20OR%20SRR10382249
[NA24149-data]: https://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/HG003_NA24149_father/NIST_HiSeq_HG003_Homogeneity-12389378/HG003Run01-13262252/
[NA24143-data]: https://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/HG004_NA24143_mother/NIST_HiSeq_HG004_Homogeneity-14572558/HG004Run01-15133132/
[NA12878-data]: https://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/NA12878/PacBio_SequelII_CCS_11kb/
[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
downloaded at
```txt
ftp://ftp.dfci.harvard.edu/pub/hli/hifiasm/submission/v0.7/
```
NA12878 was assembled with a more recent version of hifiasm and is available at
```txt
ftp://ftp.dfci.harvard.edu/pub/hli/hifiasm/NA12878-r253/
```
## Usage
@@ -145,6 +69,95 @@ and then run hifiasm as follow:
./hifiasm -o NA12878.asm -t 32 -1 pat.yak -2 mat.yak NA12878_1.fq.gz NA12878_2.fq.gz
```
## Advance features
For primary assembly, hifiasm performs purge duplication step in default. This step is designed for diploid genomes or polyploid genomes to keep one set of haplotypes without duplications. For inbred genomes or homozygous samples including only one haplotype, purge duplication step may introduce misassemblies so that it should be disabled by option `-l0`.
## Output
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
(*prefix*.r\_utg.gfa). This graph keeps all haplotype information, including
somatic mutations and recurrent sequencing errors.
2. Haplotype-resolved processed unitig graph without small bubbles
(*prefix*.p\_utg.gfa). Small bubbles might be caused by somatic mutations or noise in data,
which are not the real haplotype information.
3. Primary assembly [contig][unitig] graph (*prefix*.p\_ctg.gfa). This graph collapses different
haplotypes.
4. Alternate assembly contig graph (*prefix*.a\_ctg.gfa). This graph consists of all assemblies that
are discarded in primary contig graph.
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](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 paternal/haplotype1 contig graph (*prefix*.hap1.p\_ctg.gfa). This graph keeps the phased
paternal/haplotype1 assembly.
3. Phased maternal/haplotype2 contig graph (*prefix*.hap2.p\_ctg.gfa). This graph keeps the phased
maternal/haplotype2 assembly.
In addition, hifiasm also outputs three binary files that save all overlap information (*prefix*.ec.bin, *prefix*.ovlp.reverse.bin, *prefix*.ovlp.source.bin). 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.
## Results
Hifiasm is a standalone and lightweight assembler, which does not need external
libraries (except zlib). For large genomes, it can generate high-quality primary
assembly in several hours. Hifiasm has been tested on various large and complex datasets.
The results are as follows:
|<sub>Dataset<sub>|<sub>Size<sub>|<sub>Cov.<sub>|<sub>Asm options<sub>|<sub>CPU time<sub>|<sub>Wall time<sub>|<sub>RAM<sub>|<sub> N50<sub>|
|:---------------|-----:|-----:|:---------------------|-------:|--------:|----:|----------------:|
|<sub>[Mouse (C57/BL6J)][mouse-data]</sub>|<sub>2.6Gb</sub> |<sub>&times;25</sub>|<sub>-t48 -l0</sub> |<sub>172.9h</sub> |<sub>4.8h</sub> |<sub>76G</sub> |<sub>21.1Mb</sub>|
|<sub>[Maize (B73)][maize-data]</sub> |<sub>2.2Gb</sub> |<sub>&times;22</sub>|<sub>-t48 -l0</sub> |<sub>203.2h</sub> |<sub>5.1h</sub> |<sub>68G</sub> |<sub>36.7Mb</sub>|
|<sub>[Strawberry][strawberry-data]</sub> |<sub>0.8Gb</sub> |<sub>&times;36</sub>|<sub>-t48 -D10</sub>|<sub>152.7h</sub> |<sub>3.7h</sub> |<sub>91G</sub> |<sub>17.8Mb</sub>|
|<sub>[Frog][frog-data]</sub> |<sub>9.5Gb</sub> |<sub>&times;29</sub>|<sub>-t48</sub> |<sub>2834.3h</sub>|<sub>69.0h</sub>|<sub>463G</sub>|<sub>9.3Mb</sub>|
|<sub>[Redwood][redwood-data]</sub> |<sub>35.6Gb</sub>|<sub>&times;28</sub>|<sub>-t80</sub> |<sub>3890.3h</sub>|<sub>65.5h</sub>|<sub>699G</sub>|<sub>5.4Mb</sub>|
|<sub>[Human (CHM13)][CHM13-data]</sub> |<sub>3.1Gb</sub> |<sub>&times;32</sub>|<sub>-t48 -l0</sub> |<sub>310.7h</sub> |<sub>8.2h</sub> |<sub>114G</sub>|<sub>88.9Mb</sub>|
|<sub>[Human (HG00733)][HG00733-data]</sub>|<sub>3.1Gb</sub>|<sub>&times;33</sub>|<sub>-t48</sub> |<sub>269.1h</sub> |<sub>6.9h</sub> |<sub>135G</sub>|<sub>69.9Mb</sub>|
|<sub>[Human (HG002)][NA24385-data]</sub> |<sub>3.1Gb</sub> |<sub>&times;36</sub>|<sub>-t48</sub> |<sub>305.4h</sub> |<sub>7.7h</sub> |<sub>137G</sub>|<sub>98.7Mb</sub>|
[mouse-data]: https://www.ncbi.nlm.nih.gov/sra/?term=SRR11606870
[maize-data]: https://www.ncbi.nlm.nih.gov/sra/?term=SRR11606869
[strawberry-data]: https://www.ncbi.nlm.nih.gov/sra/?term=SRR11606867
[frog-data]: https://www.ncbi.nlm.nih.gov/sra?term=(SRR11606868)%20OR%20SRR12048570
[redwood-data]: https://www.ncbi.nlm.nih.gov/sra/?term=SRP251156
[CHM13-data]: https://www.ncbi.nlm.nih.gov/sra?term=(((SRR11292120)%20OR%20SRR11292121)%20OR%20SRR11292122)%20OR%20SRR11292123
Hifiasm also can produce high-quality fully phased assembly. We tested it on the following trio-binning datasets:
|<sub>Dataset<sub>|<sub>Cov.<sub>|<sub>CPU time<sub>|<sub>Elapsed time<sub>|<sub>RAM<sub>|<sub> N50<sub>|
|:---------------|-----:|-------:|--------:|----:|----------------:|
|<sub>[HG00733][HG00733-data], [\[father\]][HG00731-data], [\[mother\]][HG00732-data]</sub>|<sub>&times;33</sub>|<sub>269.1h</sub>|<sub>6.9h</sub>|<sub>135G</sub>|<sub>35.1Mb (paternal), 34.9Mb (maternal)</sub>|
|<sub>[HG002][NA24385-data], [\[father\]][NA24149-data], [\[mother\]][NA24143-data]</sup>|<sub>&times;36</sub>|<sub>305.4h</sub>|<sub>7.7h</sub>|<sub>137G</sub>|<sub>41.0Mb (paternal), 40.8Mb (maternal)</sub>|
|<sub>[NA12878][NA12878-data], [\[father\]][NA12891-data], [\[mother\]][NA12892-data]</sub>|<sub>&times;30</sub>|<sub>180.8h</sub>|<sub>4.9h</sub>|<sub>123G</sub>|<sub>27.7Mb (paternal), 27.0Mb (maternal)</sub>|
[HG00733-data]: https://www.ebi.ac.uk/ena/data/view/ERX3831682
[HG00731-data]: https://www.ebi.ac.uk/ena/data/view/ERR3241754
[HG00732-data]: https://www.ebi.ac.uk/ena/data/view/ERR3241755
[NA24385-data]: https://www.ncbi.nlm.nih.gov/sra?term=(((SRR10382244)%20OR%20SRR10382245)%20OR%20SRR10382248)%20OR%20SRR10382249
[NA24149-data]: https://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/HG003_NA24149_father/NIST_HiSeq_HG003_Homogeneity-12389378/HG003Run01-13262252/
[NA24143-data]: https://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/HG004_NA24143_mother/NIST_HiSeq_HG004_Homogeneity-14572558/HG004Run01-15133132/
[NA12878-data]: https://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/NA12878/PacBio_SequelII_CCS_11kb/
[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
downloaded at
```txt
ftp://ftp.dfci.harvard.edu/pub/hli/hifiasm/submission/v0.7/
```
NA12878 was assembled with a more recent version of hifiasm and is available at
```txt
ftp://ftp.dfci.harvard.edu/pub/hli/hifiasm/NA12878-r253/
```
[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