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aaranyue / quarTeT

A telomere-to-telomere toolkit for gap-free genome assembly and centromeric repeat identification
http://atcgn.com:8080/quarTeT/home.html
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Subject: Using QuarTeT GapFiller with Unplaced Scaffolds and Flanks from a related species. #42

Open Isoris opened 1 day ago

Isoris commented 1 day ago

Hello,

I would like to use QuarTeT GapFiller to fill gaps in my Clarias macrocephalus assembly chromosomes using unplaced scaffolds. I have mapped these unplaced scaffolds to a closely related species, Clarias fuscus, and obtained 50 Mb of sequence with high accuracy. However, QuarTeT AssemblyMapper outputs the results with 100 bp gaps.

My aim is to use the contigs along with the flanking regions from Clarias fuscus, making them chimeric. This way, I can run QuarTeT GapFiller with the initial chromosomes from C. macrocephalus and these modified scaffolds that include flanks from C. fuscus. The idea is to provide the necessary homology for effective gap filling, as the original assembly lacks sufficient flank homology for direct gap filling.

Would it be possible to get the output with the reference flanks from AssemblyMapper to achieve this?

Thank you!

Echoring commented 10 hours ago

I'm not sure I got your point. What you wish is when AssemblyMapper place 2 adjacent contigs, it not only use 100N to connect them but also merge some flanking sequence from the reference? This looks somehow hard to declare the border. If you want a longer flanking sequence to reach the homologous region with reference, can it be achieved by use a large -f option?

Isoris commented 6 hours ago

More like I want to also have another output with the contig that was mapped to the reference + the two flanking sequences of the length -f on both sides?

On Sun, Oct 20, 2024, 9:38 AM Echoring @.***> wrote:

I'm not sure I got your point. What you wish is when AssemblyMapper place 2 adjacent contigs, it not only use 100N to connect them but also merge some flanking sequence from the reference? This looks somehow hard to declare the border. If you want a longer flanking sequence to reach the homologous region with reference, can it be achieved by use a large -f option?

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