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Results tagged with benchmarking
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user 298
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?
2
votes
Accepted
Introducing a fixed number of random substitutions in a sequence
Here's a slightly different approach that should be more efficient. The core of the idea is to have two functions, one which changes a given nucleotide to something other than what it was, and another …
- 10.6k
3
votes
Remove/delete sequences by ID from multifasta
Using the FastaToTbl and TblToFasta scripts I have posted before, you can do:
FastaToTbl file.fa | grep -vwf ids.txt | TblToFasta > file.2.fa
- 10.6k
1
vote
Accepted
efficient counting of dinucleotides/trinucleotides on fastq reads?
Well, I'm sure you can find a more efficient approach, but here's a simplistic solution using standard UNIX tools:
zcat file.fastq.gz | grep CGC |
awk -F'CGC' 'NR%4==2{a[NF-1]++}END{for(i in a){ …
- 10.6k