Questions tagged [benchmarking]

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?

Filter by
Sorted by
Tagged with
1 vote
0 answers

Benchmarking for variant identification using RNA-seq data

I am in need to benchmark the variant identification pipeline which uses RNA seq data alone without any matched-normal. I would like to know the reference dataset (and the pipeline on which the ...
Ahkam's user avatar
  • 11
1 vote
1 answer

Refactoring a script mapping ID to sequence

I wrote simple Python script which has an excessive run time, notably when using large data sets. For example a data set of 1 000 000 sequences. I am seeking assistance refactoring the code and would ...
MTG's user avatar
  • 47
1 vote
2 answers

Improving list speed: glycosylation example

I discussed a question with @gaspanic Python/Biopython - Replace amino acid residue on MSA with "z" from a list of unaligned positions . The issue emerged was speeding up lists in Python. ...
M__'s user avatar
  • 11.2k
1 vote
1 answer

Challenging benchmarks for supervised learning on sparse scRNA-seq data

One challenging aspect of modeling scRNA-seq data is data sparsity, that is, scRNA-seq measurements typically suffer from large fractions of observed zeros (i.e. dropouts), where a given gene in a ...
rvinas's user avatar
  • 123
3 votes
2 answers

Gold standard benchmark

This page is claimed to contain a gold standard benchmark for viral genome assembly. The claim is here: ...
juanjo75es's user avatar
8 votes
9 answers

Remove/delete sequences by ID from multifasta

I have a fasta file like this: >Id1 ATCCTT >Id2 ATTTTCCC >Id3 TTTCCCCAAAA >Id4 CCCTTTAAA I want to delete sequences that have the following IDs. <...
andresito's user avatar
  • 375
2 votes
1 answer

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,...
719016's user avatar
  • 2,294
21 votes
8 answers

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 ...
conchoecia's user avatar
  • 3,141
12 votes
8 answers

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 <...
terdon's user avatar
  • 9,442
20 votes
12 answers

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 ...
winni2k's user avatar
  • 2,206
13 votes
4 answers

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 ...
Konrad Rudolph's user avatar
21 votes
10 answers

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 ...
Kamil S Jaron's user avatar