Indexing large genome failed

lh3 / bwa

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

GNU General Public License v3.0

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Indexing large genome failed #413

Open xzhoubayer opened 8 months ago

xzhoubayer commented 8 months ago

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 commented 7 months ago

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 commented 7 months ago

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

nicolo-tellini commented 3 months ago

you might be interested on this issue #104

maybe playing with -aand -b option can help.