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[1.2.0 - Ancient Destiny] Chunk fasta reads for better parallelization for revio pacbio data #285

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DLBPointon opened this issue Mar 20, 2024 · 4 comments

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@DLBPointon
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Description of feature

The size of the revio data is huge, this needs to be split into n = (reads / 10million) files. Mapping and then merge the output.

@yumisims
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if fasta size > 10G, then split the fasta.gz into N chunks, N= round( size_of_fasta/10)
pyfasta split -n N {sample}.fasta.gz

@mcshane
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mcshane commented Mar 20, 2024

@yumisims @DLBPointon. Maybe use https://nf-co.re/modules/seqkit_split2 ?

@yumisims
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or just zcat {sample}.fasta.gz | awk '/^>/{n++} { print > ("chunk_" int(n/N) ".fasta") }'
let's see

@mcshane
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mcshane commented Mar 20, 2024

seqkit split2 is multithreaded and will output gzipped chunks

@DLBPointon DLBPointon changed the title Chunk fasta reads for better parallelization for revio pacbio data [1.2.0 - Ancient Destiny]Chunk fasta reads for better parallelization for revio pacbio data Mar 21, 2024
@DLBPointon DLBPointon changed the title [1.2.0 - Ancient Destiny]Chunk fasta reads for better parallelization for revio pacbio data [1.2.0 - Ancient Destiny] Chunk fasta reads for better parallelization for revio pacbio data Mar 21, 2024
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3 participants