Newest 'benchmarking+fastq' Questions

2 votes

1 answer

112 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,...

719016

2,364

asked Feb 22, 2018 at 10:18

13 votes

8 answers

17k 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 <...

terdon♦

10.6k

asked Jun 28, 2017 at 14:50

21 votes

12 answers

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 ...

winni2k

2,286

asked Jun 19, 2017 at 13:15

22 votes

10 answers

7k 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 ...

Kamil S Jaron

5,652

asked Jun 1, 2017 at 16:47

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