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Jellyfish internals #4

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utsavjainb opened this issue Feb 27, 2020 · 0 comments

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utsavjainb commented Feb 27, 2020 •

edited by harishankarv

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Internals of overlap parsing in jellyfish

Verify if overlap kmers are being counted (is it a kmer if it spills over 'records'?)
Jellyfish adds an 'N' character in its overlap parser after reading a 'record' in memory. Why? It is because further downstream 'N's are treated as separator to indicate new kmer (indication to stop current sliding window and start a new one), because FASTA files have 'N's too.
Verify what is the use of the non-overlap parser.

File streaming

Check if jellyfish uses streaming? Do they use file-stream operators, why do they use it?

Canonicalization

How does Jellyfish handle canonicalization?

utsavjainb assigned harishankarv and utsavjainb

harishankarv added the question label

harishankarv changed the title ~~Internals of overlap parsing in jellyfish~~ Jellyfish internals

arkivm unassigned utsavjainb

arkivm unassigned harishankarv

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