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update for r350

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chhylp123
2021-07-26 00:16:00 -04:00
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docs/source/interpreting-output.rst
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@@ -12,9 +12,9 @@ Output files
In general, hifiasm generates the following assembly graphs in the GFA format:
* ```prefix`.r_utg.gfa``: haplotype-resolved raw unitig graph. This graph keeps all haplotype information.
* ```prefix`.p_utg.gfa``: haplotype-resolved processed unitig graph without small bubbles. Small bubbles might be caused by somatic mutations or noise in data, which are not the real haplotype information. Hifiasm automatically pops such small bubbles based on coverage. The option ``--purge-cov`` affects the result. See :ref:`homozygous coverage setting <homcov>` for more details. In addition, the option ``-p`` forcedly pops bubbles.
* ```prefix`.p_utg.gfa``: haplotype-resolved processed unitig graph without small bubbles. Small bubbles might be caused by somatic mutations or noise in data, which are not the real haplotype information. Hifiasm automatically pops such small bubbles based on coverage. The option ``--hom-cov`` affects the result. See :ref:`homozygous coverage setting <homcov>` for more details. In addition, the option ``-p`` forcedly pops bubbles.
* ```prefix`.p_ctg.gfa``: assembly graph of primary contigs. This graph includes a complete assembly with long stretches of phased blocks.
* ```prefix`.a_ctg.gfa``: assembly graph of alternate contigs. This graph consists of all assemblies that are discarded in primary contig graph.
* ```prefix`.a_ctg.gfa``: assembly graph of alternate contigs. This graph consists of all contigs that are discarded in primary contig graph.
* ```prefix`.*hap*.p_ctg.gfa``: phased contig graph. This graph keeps the phased contigs.
@@ -98,5 +98,5 @@ Hifiasm prints several information for quick debugging, including:
.. _homcov:
* k-mer plot: showing how many k-mers appear a certain number of times. For homozygous samples, there should be one peak around read coverage. For heterozygous samples, there should two peaks, where the smaller peak is around the heterozygous read coverage and the larger peak is around the homozygous read coverage. For example, `issue10 <https://github.com/chhylp123/hifiasm/issues/10#issuecomment-616213684>`_ indicates the heterozygous read coverage and the homozygous read coverage are 28 and 57, respectively. `Issue49 <https://github.com/chhylp123/hifiasm/issues/49#issue-729106823>`_ is another good example. Weird k-mer plot like `issue93 <https://github.com/chhylp123/hifiasm/issues/93#issue-852259042>`_ is often caused by insufficient coverage or presence of contaminants.
* homozygous coverage: coverage threshold for homozygous reads. Hifiasm prints it as: ``[M::purge_dups] purge duplication coverage threshold: X``. Without setting the option ``--purge-cov``, the homozygous coverage threshold determined by hifiasm is: ``X/1.25``. If it is not around homozygous coverage, the final assembly might be either too large or too small. To fix this issue, please set ``--purge-cov`` to homozygous coverage.
* number of het/hom bases: how many bases in unitig graph are heterozygous and homozygous during Hi-C phased assembly. Hifiasm prints it as: ``[M::stat] # heterozygous bases: X; # homozygous bases: Y``. Given a heterozygous sample, if there are much more homozygous bases than heterozygous bases, hifiasm fails to identify correct coverage threshold for homozygous reads. In this case, please set ``--purge-cov`` to homozygous coverage.
* homozygous coverage: coverage threshold for homozygous reads. Hifiasm prints it as: ``[M::purge_dups] homozygous read coverage threshold: X``. If it is not around homozygous coverage, the final assembly might be either too large or too small. To fix this issue, please set ``--hom-cov`` to homozygous coverage.
* number of het/hom bases: how many bases in unitig graph are heterozygous and homozygous during Hi-C phased assembly. Hifiasm prints it as: ``[M::stat] # heterozygous bases: X; # homozygous bases: Y``. Given a heterozygous sample, if there are much more homozygous bases than heterozygous bases, hifiasm fails to identify correct coverage threshold for homozygous reads. In this case, please set ``--hom-cov`` to homozygous coverage.