Questions tagged [benchmarking]

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votes
1answer
75 views

efficient counting of dinucleotides/trinucleotides on fastq reads?

What's an efficient way of counting of dinucleotides/trinucleotide pattern on fastq.gz file reads? I know there are tools like seqtk that will be very efficient at reading through the .fastq.gz files,...
15
votes
7answers
6k views

What is the fastest way to get the reverse complement of a DNA sequence in python?

I am writing a python script that requires a reverse complement function to be called on DNA strings of length 1 through around length 30. Line profiling programs indicate that my functions spend a ...
10
votes
7answers
7k views

Fast way to count number of reads and number of bases in a fastq file?

I am looking for a tool, preferably written in C or C++, that can quickly and efficiently count the number of reads and the number of bases in a compressed fastq file. I am currently doing this using <...
16
votes
12answers
1k views

Random access on a FASTQ file

I would like to select a random record from a large set of n unaligned sequencing reads in log(n) time complexity (big O ...
12
votes
4answers
438 views

How do I efficiently subset a very large line-based file?

This has come up repeatedly recently: I have a very large text file (in the order of several GiB) and I need to perform line-based subsetting for around 10,000 lines. There exist solutions for ...
7
votes
0answers
299 views

Improving consensus assembly from UMI-tagged nanopore reads

The Albertsen lab has recently put out a competition/challenge for read error correction I only found out about this today, and I think the conference where high-ranking participants were going to be ...
17
votes
10answers
3k views

What is the fastest way to calculate the number of unknown nucleotides in FASTA / FASTQ files?

I used to work with publicly available genomic references, where basic statistics are usually available and if they are not, you have to compute them only once so there is no reason to worry about ...