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update for r350

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chhylp123
2021-07-26 00:16:00 -04:00
parent b14f894160
commit 321acb2d8a
12 changed files with 241 additions and 130 deletions
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docs/source/pa-assembly.rst
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@@ -32,7 +32,7 @@ In this example, the partially phased contigs are written to ``NA12878.asm.bp.ha
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``.
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.
In this case, please set ``--purge-cov`` to homozygous coverage. See :ref:`p-large` for more details.
In this case, please set ``--hom-cov`` to homozygous coverage. See :ref:`p-large` for more details.
Produce primary/alternate assemblies
@@ -42,6 +42,6 @@ To get primary/alternate assemblies, the option ``--primary`` should be set::
hifiasm -o NA12878.asm --primary -t 32 NA12878.fq.gz
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 ``--purge-cov`` should
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
be helpful if the primary assembly is too large. See :ref:`p-large` for more details.