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amplab / snap

Scalable Nucleotide Alignment Program -- a fast and accurate read aligner for high-throughput sequencing data
https://www.microsoft.com/en-us/research/project/snap/
Apache License 2.0
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Has any version can index fasta file more large than 4.2G？ #122

Closed Winjor closed 3 years ago

Winjor commented 4 years ago

Hi，I see the same question in google group，but not solved yet. Are there any way or any version of SNAP can do that?
By the way, I see the version is updated to 1.0beta.24 in master from update log and actively in some branches, any latest version will release？

bolosky commented 4 years ago

Any version of SNAP should be able to index a genome of any practical size. If it’s bigger than 232 bases, or really even close to that, you’ll need to say -locationSize 5 when you build the index. That’s even true for the human genome if you use a small seed size (for reasons too complicated to explain here). If you try to index something too big, you should get an error message telling you to increase -locationSize. If you have something truly huge (like 240 bases) and the memory to hold such an index, maybe you’ll need -locationSize 6.

We’re working on a set of major updates to SNAP. In particular, we’ve added affine gap scoring with which SNAP calls indels with about the same precision and recall as bwa-mem, but much, much faster. I’m not sure of the schedule for actually releasing it, but it shouldn’t be too long.

--Bill

From: Winjor Chen notifications@github.com Sent: Tuesday, September 24, 2019 12:50 AM To: amplab/snap snap@noreply.github.com Cc: Subscribed subscribed@noreply.github.com Subject: [amplab/snap] Has any version can index fasta file more large than 4.2G？ (#122)

Hi，I see the same question in google group，but not solved yet. Are there any way or any version of SNAP can do that? By the way, I see the version is updated to 1.0beta.24 in master from update log and actively in some branches, any latest version will release？

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