Questions tagged [benchmarking]
The benchmarking tag has no usage guidance.
9
questions
1
vote
1answer
54 views
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 ...
2
votes
1answer
45 views
Gold standard benchmark
This page is claimed to contain a gold standard benchmark for viral genome assembly.
https://github.com/cbg-ethz/5-virus-mix
The claim is here:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5411778/
&...
8
votes
9answers
15k views
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.
<...
2
votes
1answer
88 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,...
20
votes
8answers
8k 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 ...
12
votes
8answers
11k 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 <...
20
votes
12answers
2k 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 ...
13
votes
4answers
687 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 ...
20
votes
10answers
5k 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 ...
