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Indexing large genome failed #413

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xzhoubayer opened this issue Mar 14, 2024 · 3 comments
Open

Indexing large genome failed #413

xzhoubayer opened this issue Mar 14, 2024 · 3 comments

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@xzhoubayer
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Indexing onion/garlic genome failed since the genome is 16Gb and two chromosomes are longer than 2.1 Gb.
Does BWA has a limit for sequence length?
@bpanda-dev
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3. Does BWA work on reference sequences longer than 4GB in total?
Yes. Since 0.6.x, all BWA algorithms work with a genome with total length over 4GB. However, individual chromosome should not be longer than 2GB.

Source.

@xzhoubayer
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Does it have limit for the length of each sequence/contig/chromosome?

@nicolo-tellini
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nicolo-tellini commented Aug 12, 2024 •
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you might be interested on this issue #104

maybe playing with -a and -b option can help.

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@bpanda-dev @nicolo-tellini @xzhoubayer