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Results tagged with benchmarking
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user 1769
Benchmarking problems relate to problems where efficiency is key, beyond just solving a problem itself. What's the fastest or most efficient way to solve a problem?
6
votes
What is the fastest way to calculate the number of unknown nucleotides in FASTA / FASTQ files?
Additionally it would be good to use a specific file for benchmarking which actually has Ns, because you'll get some quite interesting execution time differences with some methods counting the more frequently … Benchmarking another alternative pigz grep variant appears to take more or less the same time as the tr based variant:
time pigz -dc SRR077487_2.filt.fastq.gz | awk 'NR%4==2{print $1}' | grep -o N | wc …
- 1,069
7
votes
Fast way to count number of reads and number of bases in a fastq file?
pigz | awk | wc is the fastest method
First off for benchmarks with FASTQ it's best to use a specific real-world example with a known answer. I've chosen this file:
ftp://ftp.1000genomes.ebi.ac.uk/ …
- 1,069