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baoxingsong / AnchorWave

Sensitive alignment of genomes with high sequence diversity, extensive structural polymorphism and whole-genome duplication variation
MIT License
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Is it possible to output whole genome alignment in paf format? #30

Closed Yutang-ETH closed 2 years ago

Yutang-ETH commented 2 years ago

Hi Baoxing,

Nice to meet you. I am Yutang, a doctoral student studying forage grass at ETH-Zurich. I think leveraging gene collinearity for whole genome alignment is definitely a wonderful idea, especially for plants with very complicated genomes. I am just wondering, could we get a paf formatted file of alignment from AnchorWave? I am asking this because the pangenome pipeline pggb could accecpt a paf as input.

Thank you very much.

Best wishes, Yutang

baoxingsong commented 2 years ago

Thanks, Yutang,

  1. I am not familiar with the PAF format. We provide guidance in reformating the MAF format to the SAM/BAM format. I guess there are some tools to reformat a SAM file to a PAF file?
  2. The PHG pipeline (https://bitbucket.org/bucklerlab/practicalhaplotypegraph/wiki/Home) works well together with AnchorWave. Might deserve a try?
baoxingsong commented 2 years ago

Thanks, Yutang,

  1. I am not familiar with the PAF format. We provide guidance in reformating the MAF format to the SAM/BAM format. I guess there are some tools to reformat a SAM file to a PAF file?
  2. The PHG pipeline (https://bitbucket.org/bucklerlab/practicalhaplotypegraph/wiki/Home) works well together with AnchorWave. Might deserve a try?
Yutang-ETH commented 2 years ago

Thank you very much, Baoxing,

I see, yes, we can convert sam to paf and thank you very much for sharing the PHG pipeline with me, it is promising. I will have a look. Best wishes, Yutang