IPA (Improved Phased Assembly) output questions
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7 months ago
slin023 • 0

Hello, I just finished IPA assembly for my genome assembly (https://github.com/PacificBiosciences/pbipa), but I received two output files. The tutorial didn't mention anything, I checked two fasta files, one is

  1. final.a_ctg.fasta, it has id named " >hap_ctg.000084F_1 HAPLOTIG", "hap", I assume is haploid?

The other is 2.final.p_ctg.fasta, it has id named ">ctg.000071F_1"

Can someone explain the difference between two files, and what the letters and numbers mean, please?

(ex: hap_ctg.000084F_1, what is ctg? what is 00084? what is F_1?, for two output files, what do "a" and "p" represent in fasta name?)

Assembly genome PacBio • 324 views
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Entering edit mode
7 months ago
h.mon 32k

Some of this information can be found at an old Falcon documentation page:

The final output of this step is a fasta file of all of the primary contigs, p_ctg.fa as well as an associated contig fasta file, a_ctg.fa that consists of all of the structural variants from the primary contig assembly.

A cursory look at the wiki revealed no clues, I think you could open an issue at the IPA github page asking for better documentation - just be sure to search extensively before doing so.

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