Questions tagged [k-mer]

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

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1
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1answer
33 views

Truble to run a multiprocessing kmer count script

Hi there I have this code: ...
1
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1answer
53 views

Significance of k-mer length in COVID-19 sequence analysis?

I'm getting started in biology and bioinformatics with sequencing the SARS-Cov-2 or Coronavirus genome. I'm interested in this code which identifies k-mers in the genome: ...
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0answers
35 views

Will using smaller kmers help get larger contigs? If not, then what?

I've been using MEGAHIT to assemble metagenomes, with particular focus on specific genomic areas. Sometimes all I get is gene fragments or pathway fragments (eg. if I know that genes A, B, C, D and E ...
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3answers
80 views

K means clustering, would PCA be a better option?

I have the data below. I need to use a clustering method to classify them and into categories of "Heterozygotote, Allele 1, Allele 2 and No Call. The values in RFU1 and RFU2 are used to determine the ...
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0answers
16 views

Chaos game representation to calculate 3 and 4mer result in a blank plot

I need to plot the 3-mer and 4-mer using the Chaos game representation for which I have referred the tutorial available at https://towardsdatascience.com/chaos-game-representation-of-a-genetic-...
4
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1answer
84 views

Generating DNA sequences with constraints

I would like some advice on potential strategies to address the following problem. I want to write a program that will generate DNA sequences that are optimized on two constraints based on an input ...
1
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2answers
245 views

mapping heteryzygous kmers on a genome

I have a set (a couple of millions) of kmer pairs of known length (usually 21) that I know that are heterozygous in the middle nucleotide. For instance: ...
3
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1answer
274 views

python does not quit when the input file is too big

I have a script that extracts the set of unique kmer pairs from a kmer dump file (& then using them downstream to guess ploidy). The script seems to work correctly (it's reporting a meaningful ...
10
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1answer
491 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 ...
3
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0answers
111 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] ...
8
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2answers
1k 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
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1answer
296 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. ...
6
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1answer
76 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 ...
9
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1answer
312 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 ...
7
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2answers
965 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 ...
8
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3answers
475 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-...
7
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2answers
525 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 ...
7
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1answer
1k 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
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1answer
219 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
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2answers
2k 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
208 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.
3
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1answer
140 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 ....
4
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1answer
155 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 (...
7
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2answers
7k 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 ...
8
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3answers
129 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 ...
31
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2answers
1k views

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

Why do some assemblers like SOAPdenovo2 or Velvet require an odd-length k-mer size for the construction of de Bruijn graph, while some other assemblers like ABySS are fine with even-length k-mers?
14
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3answers
353 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 ...
22
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4answers
1k 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 ...