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32 lines
2.0 KiB
ReStructuredText
32 lines
2.0 KiB
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.. _trio-assembly:
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Trio-binning Assembly
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=====================
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When parental short reads are available, hifiasm can also generate a pair of haplotype-resolved assemblies with trio binning. To perform such assembly, you need to count k-mers first with `yak <https://github.com/lh3/yak>`_ and then do assembly::
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yak count -k31 -b37 -t16 -o pat.yak paternal.fq.gz
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yak count -k31 -b37 -t16 -o mat.yak maternal.fq.gz
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hifiasm -o NA12878.asm -t 32 -1 pat.yak -2 mat.yak NA12878.fq.gz
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Here ``NA12878.asm.hap1.p_ctg.gfa`` and ``NA12878.asm.hap2.p_ctg.gfa`` give the assemblies for two haplotypes. In the binning mode, hifiasm does not purge haplotig duplicates by default. Because hifiasm reuses saved overlaps, you can generate both primary/alternate assemblies and trio binning assemblies with::
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hifiasm -o NA12878.asm --primary -t 32 NA12878.fq.gz 2> NA12878.asm.pri.log
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hifiasm -o NA12878.asm -t 32 -1 pat.yak -2 mat.yak /dev/null 2> NA12878.asm.trio.log
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The second command line will run much faster than the first. The phasing switch error rate and hamming error rate are able to be evaluated quickly by `yak <https://github.com/lh3/yak>`_::
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yak trioeval -t16 pat.yak mat.yak assembly.fa
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The W-line and H-line reported by ``yak trioeval`` indicate switch error rate and hamming error rate respectively::
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W 26714 3029448 0.008818
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H 24315 3029885 0.008025
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For this example, the switch error rate is 0.8818% and the hamming error rate is 0.8025%.
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In rare cases, a potential issue is that a few contigs may misjoin two haplotypes. For example, half of a contig come from mother while another half come from father. Such misjoined contigs can be fixed by
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manually breaking. The coordinates of problematic regions can be found by A-lines in GFA file or ``yak trioeval -e``. However, if there are many misjoined contigs or the switch/hamming error rate reported by ``yak trioeval`` is very high, users should check if the parental data is correct (see `example <https://github.com/chhylp123/hifiasm/issues/130#issuecomment-862347943>`_ for more details).
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