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Questions tagged [k-mer]

for questions related to k-mer based algorithms, data structures, or concepts

6
votes
1answer
287 views

What is the most compact data structure for canonical k-mers with the fastest lookup time?

edit: Results are current as of Dec 4, 2018 13:00 PST. Background K-mers have many uses in bioinformatics, and for this reason it would be useful to know the most RAM-efficient and fastest way to ...
4
votes
0answers
59 views

Histosketch vs Count-Min sketch: preserving similarity

A preprint describing a new tool and its application to microbiome analysis was recently published in bioRxiv[1]. At the core of this new tool, HULK, is a new data structure called a histosketch[2] ...
7
votes
1answer
192 views

estimate genome size: kmer-based approach from PacBio reads

Can anyone suggest a software/method for kmer analysis using PacBio reads (RSII)? Something similar to Jellyfish, that I saw in a nice tutorial - but must be suitable for long, noisy reads. ...
8
votes
1answer
116 views

Counting repeated kmers sequences that match at least x % of reads sequence

Working on a fastQ file, I would like to get the occurrences of repeated sequences for all possible kmers of a given length that cover at least 90% of the read's length for the whole data set. ...
7
votes
1answer
57 views

How to efficiently compute the exact percentage of non-unique k-mers in a genome for given k?

I'm looking for some software that can "efficiently" (time and memory) compute the exact percentage of non-unique k-mers in a genome for given k. I don't need the k-mers or the abundances itself, I ...
7
votes
1answer
136 views

How to get the count of each kmer past 255 using khmer

I have a Fastq file and I want to get the exact count of each possible kmer from this file. On a previous post called How to use khmer to count k-mers? Daniel Standage proposed a custom script based ...
6
votes
2answers
321 views

Stranded vs. unstranded library preparation protocols in RNAseq

I've been reading this paper lately: Sailfish Enables Alignment-Free Isoform Quantification from RNA-Seq Reads Using Lightweight Algorithms I don't really understand the second paragraph under ...
7
votes
3answers
271 views

How to calculate the memory usage of storing kmers in RAM

I want to write a program in C++ that stores kmers in a hash or in a trie. How can I calculate how much RAM I would need for each type of data structure? For this application my kmers are strand-...
5
votes
2answers
169 views

How to write a hash function for canonical kmers?

This question is a follow up from How do kmer counters determine which kmer is 'canonical'?. In that question we learned that kmer counting programs use a 2-bit hash function to internally represent ...
5
votes
1answer
234 views

How do kmer counters determine which kmer is 'canonical'?

When counting canonical kmers, ie kmers in which both the forward and reverse complement of a sequence are treated as identical, how do kmer counting programs decide which kmer to use as the canonical ...
7
votes
1answer
100 views

server for finding kmers in set of sequences

Is there a server/website somewhere where I can submit a list of DNA/RNA sequences and find the list of kmers hits and organisms where it's found? I checked the kraken website, but they don't have a ...
8
votes
2answers
438 views

Formula for k-mer coverage

Let $C$ be base coverage, $R$ is the length of reads and $K$ is the length of $k$-mer. Then $k$-mer coverage $C_k$ can be computed as $C_k = C\cdot(R - K + 1)/R$. Could someone please explain why is ...
12
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2answers
132 views

Is there a standard k-mer count file format?

I am doing a research project involving calculating k-mer frequencies and I am wondering if there is any standard file format for storing k-mer counts.
2
votes
1answer
94 views

Why do BLASTn and prokka not seem to be searching the whole fasta file?

When I use blastn and prokka (I will detail exactly how I did so below) on a 2.8 million bp fasta file I get output start/end numbers that do not seem to cover the entire genome. Starting with a ....
3
votes
1answer
98 views

Preparing binary matrix data for Scikit classification algorithms

I made this post in regular stack overflow but I was told about this awesome feature by @nbryans. I am a researcher (my programming knowledge is small) conducting analysis on a set of antibiotic (...
6
votes
2answers
2k views

How to use Python to count k-mers?

I have some FASTQ sequence files and a FASTA file for some regions I'm interested in. I would like: Build an index for the FASTA file Use the index to count number of k-mers occurred in my sequence ...
7
votes
3answers
87 views

Have DNA motifs 6-12bp long, trying to get conservation scores

I have about 200 short nucleotide motifs (6-12 bp in length) from the human genome, and I'm trying to see how conserved they are across vertebrates. I was thinking that I'd need to make a bed file ...
20
votes
1answer
418 views

Why do some assemblers require an odd-length kmer for the construction of De Brujin graphs?

Why do some assemblers like SOAPdenovo2 or Velvet require an odd-length kmer for the construction of De Brujin graph, while some other assemblers like ABySS are fine with even-length kmers?
13
votes
3answers
187 views

How to make a distinction between the “classical” de Bruijn graph and the one described in NGS papers?

In Computer Science a De Bruijn graph has (1) m^n vertices representing all possible sequences of length n over ...
21
votes
4answers
732 views

Are there any rolling hash functions that can hash a DNA sequence and its reverse complement to the same value?

A common bioinformatics task is to decompose a DNA sequence into its constituent k-mers and compute a hash value for each k-mer. Rolling hash functions are an appealing solution for this task, since ...