KMA statistics

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Citations per year

Number of citations per year for the bioinformatics software tool KMA
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Tool usage distribution map

This map represents all the scientific publications referring to KMA per scientific context
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Associated diseases

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Popular tool citations

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Protocols

KMA specifications

Information


Unique identifier OMICS_31606
Name KMA
Alternative name k-mer alignment
Interface Web user interface
Restrictions to use None
Input format FASTA,FASTQ
Output data Some consensus sequences and a result overview.
Computer skills Basic
Stability Stable
Maintained Yes

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Maintainer


Additional information


https://cge.cbs.dtu.dk/services/KMA/instructions.php

Information


Unique identifier OMICS_31606
Name KMA
Alternative name k-mer alignment
Software type Application/Script
Interface Command line interface
Restrictions to use None
Output data Some consensus sequences and a result overview.
Operating system Unix/Linux, Mac OS, Windows
Programming languages C
License Apache License version 2.0
Computer skills Advanced
Stability Stable
Requirements
C-compiler, zlib development files
Maintained Yes

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Versioning


No version available

Maintainer


Additional information


https://cge.cbs.dtu.dk/services/KMA/instructions.php

Publication for k-mer alignment

KMA citations

 (4)
library_books

Enhancing the Resolution of Rumen Microbial Classification from Metatranscriptomic Data Using Kraken and Mothur

2017
Front Microbiol
PMCID: 5725470
PMID: 29270165
DOI: 10.3389/fmicb.2017.02445

[…] o overcome the technical challenges posed by the analysis of massively paralleled, high-throughput sequencing data (; ). These bioinformatics tools make use of several techniques (e.g., read mapping, k-mer alignment, and composition analysis) () and can be categorized into two distinct groups: (1) programs that use all available genome sequences (), also called assignment-first approaches () (e.g. […]

library_books

Flavivirus and Filovirus EvoPrinters: New alignment tools for the comparative analysis of viral evolution

2017
PLoS Negl Trop Dis
PMCID: 5489223
PMID: 28622346
DOI: 10.1371/journal.pntd.0005673

[…] quence and the intra-species database genomes. Although BLAT alignments are significantly faster than Clustal comparisons, aligning bases at or near sequence ends are often missed due to insufficient K-mer alignment target lengths. Pairwise alignments are then converted to distinguish between aligning bases (upper case) and non-aligning bases (lower case) within the input sequence for each compari […]

library_books

Assessment of Common and Emerging Bioinformatics Pipelines for Targeted Metagenomics

2017
PLoS One
PMCID: 5215245
PMID: 28052134
DOI: 10.1371/journal.pone.0169563

[…] d together by the hierarchical clustering. CLARK is the assignment-first pipeline able to identify the highest amount of reads, especially at the genus level (). One Codex and Kraken, having the same k-mer alignment + LCA algorithmic approach, have similar behaviors. One Codex OC is not able to identify many reads (unclassified) because of the One Codex 28k database, as shown in the previous secti […]

call_split

Complete Genome Sequences of Two Bordetella hinzii Strains Isolated from Humans

2015
Genome Announc
PMCID: 4551878
PMID: 26316634
DOI: 10.1128/genomeA.00965-15
call_split See protocol

[…] g genes and 64 tRNAs in F582 and 4,467 protein-coding genes and 66 tRNAs in H568. Both genomes contain three rRNA operons. A comparison of the two genomes by read mapping in CLC Genomics Workbench or k-mer alignment with kSNP (version 3.0) () revealed 8,926 to 9,688 core single-nucleotide polymorphisms (SNPs), depending on the method of identification. The two sequences also include several strain […]


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KMA institution(s)
Department of Bioinformatics, Technical University of Denmark, Lyngby, Denmark; Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Lyngby, Denmark
KMA funding source(s)
Supported by the European Union’s Horizon 2020 research and innovation programme under grant agreement no 643476 (COMPARE) and the Center for Genomic Epidemiology (Grant 09–067103/DSF).

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