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48 lines
3.0 KiB
ReStructuredText
48 lines
3.0 KiB
ReStructuredText
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.. _pa-assembly:
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HiFi-only Assembly
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==================
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A typical hifiasm command line looks like::
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hifiasm -o NA12878.asm -t 32 NA12878.fq.gz
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where ``NA12878.fq.gz`` provides the input reads, ``-t`` sets the number of CPUs in
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use and ``-o`` specifies the prefix of output files. Input sequences should be FASTA
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or FASTQ format, uncompressed or compressed with gzip (.gz). The quality scores of reads
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in FASTQ are ignored by hifiasm. Hifiasm outputs assemblies in `GFA <https://github.com/pmelsted/GFA-spec/blob/master/GFA-spec.md>`_ format.
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At the first run, hifiasm saves corrected reads and overlaps to disk as ``NA12878.asm.*.bin``. It reuses the saved results to avoid the time-consuming all-vs-all overlap calculation next time. You may specify ``-i`` to ignore precomputed overlaps and redo overlapping from raw reads. You can also dump error corrected reads in FASTA and read overlaps in PAF with::
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hifiasm -o NA12878.asm -t 32 --write-paf --write-ec /dev/null
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Hifiasm purges haplotig duplications by default. For inbred or homozygous genomes, you may disable purging with option ``-l0``. Old HiFi reads may contain short adapter sequences at the ends of reads. You can specify ``-z20`` to trim both ends of reads by 20bp. For small genomes, use ``-f0`` to disable the initial bloom filter which takes 16GB memory at the beginning. For genomes much larger than human, applying ``-f38`` or even ``-f39`` is preferred to save memory on k-mer counting.
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Produce two partially phased assemblies
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---------------------------------------
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Since v0.15, hifiasm produces two sets of partially phased contigs in default like::
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hifiasm -o NA12878.asm -t 32 NA12878.fq.gz
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In this example, the partially phased contigs are written to ``NA12878.asm.bp.hap*.p_ctg.gfa``.
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This pair of files can be thought to represent the two haplotypes in a diploid genome, though with occasional switch errors. The frequency of switches is determined by the heterozygosity of the input sample. Hifiasm also writes the primary contigs to ``NA12878.asm.bp.p_ctg.gfa``.
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For samples with high heterozygosity rate, a common issue is that one set of partially phased contigs is much larger than another set. To fix this issue, please set smaller value for ``-s`` (default: 0.55). Another possibility is that hifiasm misidentifies coverage threshold for homozygous reads.
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In this case, please set ``--hom-cov`` to homozygous coverage. See :ref:`p-large` for more details.
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Produce primary/alternate assemblies
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------------------------------------
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To get primary/alternate assemblies, the option ``--primary`` should be set::
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hifiasm -o NA12878.asm --primary -t 32 NA12878.fq.gz
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The primary contigs and the alternate contigs are written to ``NA12878.asm.p_ctg.gfa`` and ``NA12878.asm.a_ctg.gfa``, respectively. For inbred or homozygous genomes, the primary/alternate assemblies can be also produced by ``-l0``. Similarly, turning ``-s`` or ``--hom-cov`` should
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be helpful if the primary assembly is too large. See :ref:`p-large` for more details.
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