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Merge pull request #4 from lh3/update-readme

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Changed the description of the output
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Heng Li
2020-01-04 12:56:52 -05:00
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README.md
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@@ -10,24 +10,25 @@ cd hifiasm && make
## Introduction ## Introduction
Hifiasm is an ultrafast haplotype-resolved de novo assembler based on PacBio Hifiasm is a fast haplotype-reserved de novo assembler for PacBio
Hifi reads. Unlike most existing assemblers, hifiasm starts from uncollapsed Hifi reads. Unlike most existing assemblers, hifiasm starts from uncollapsed
genome. Thus, it is able to keep the haplotype information as much as possible. 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 The input of hifiasm is the PacBio Hifi reads in fasta/fastq format, and its
outputs consist of: outputs consist of:
1. Haplotype-resolved raw [unitig][unitig] graph in [GFA][gfa] format 1. Haplotype-resolved raw [unitig][unitig] graph in [GFA][gfa] format
(hifiasm.asm.r\_utg.gfa by default). This graph keeps all haplotype information. (*prefix*.r\_utg.gfa). This graph keeps all haplotype information, including
2. Haplotype-resolved processed [unitig][unitig] graph in [GFA][gfa] format somatic mutations and recurrent sequencing errors.
without small bubbles (hifiasm.asm.p\_utg.gfa by default). Small bubbles might be 2. Haplotype-resolved processed unitig graph without small bubbles
caused by somatic mutations or noise in data, which are not the real haplotype information. (*prefix*.p\_utg.gfa). This is usually the preferred output for highly
3. Primary assembly [contig][unitig] graph in [GFA][gfa] format heterozygous genomes.
(hifiasm.asm.p\_ctg.gfa by default). 3. Primary assembly [contig][unitig] graph (*prefix*.p\_ctg.gfa). This is the
4. Alternate assembly [contig][unitig] graph in [GFA][gfa] format preferred output for inbred strains or human. For highly heterozygous
(hifiasm.asm.a\_ctg.gfa by default). genomes, this graph may represent multiple haplotypes. We plan to change
5. Haplotype-aware error corrected reads in fasta format (hifiasm.asm.ec.fa by this to represent one set of haplotypes.
default). 4. Alternate assembly contig graph (*prefix*.a\_ctg.gfa).
6. All-to-all overlaps in [paf][paf] format (hifiasm.asm.ovlp.paf). 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 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 chromosome-level high-quality assembly in the near future. In addition, hifiasm
@@ -98,10 +99,10 @@ have further questions, please raise an issue at the issue page.
1. For genome with low heterozygous rate, hifiasm only outputs 1. For genome with low heterozygous rate, hifiasm only outputs
haplotype-resolved assembly graph, instead of the phased chromosome-level haplotype-resolved assembly graph, instead of the phased chromosome-level
assembly (**will support such output in the near future**). assembly (will support such output in future).
2. For different species, hifiasm outputs different assembly graphs, which are not easy to use. 2. For different species, hifiasm outputs different assembly graphs, which are not easy to use.
**Hifiasm will generate a universal haplotype-resolved contig graph for all species in the near future.** Hifiasm will generate a universal haplotype-resolved contig graph for all species in future.
3. The running time and memory usage should be further reduced. 3. The running time and memory usage should be further reduced.