Tag: K-mer

gkm-DNN – gapped k-mer deep neural network

gkm-DNN

:: DESCRIPTION

gkm-DNN is a software which uses gapped k-mer frequency vector (gkm-fv) as input to train neural networks. gkm-DNN is designed for classification but can be easily extended to other problems such as regression and ranking.

::DEVELOPER

Shihua Zhang’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • R

:: DOWNLOAD

gkm-DNN

:: MORE INFORMATION

Citation

Cao Z, Zhang S.
Probe Efficient Feature Representation of Gapped K-mer Frequency Vectors from Sequences Using Deep Neural Networks.
IEEE/ACM Trans Comput Biol Bioinform. 2020 Mar-Apr;17(2):657-667. doi: 10.1109/TCBB.2018.2868071. Epub 2018 Aug 31. PMID: 30183639.

KAnalyze 2.0.0 – DNA/RNA Sequence K-mer Toolkit

KAnalyze 2.0.0

:: DESCRIPTION

KAnalyze is a Java toolkit designed to convert DNA and RNA sequences into k-mers.

::DEVELOPER

Vannberg Lab 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Java

:: DOWNLOAD

 KAnalyze

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Mar 18.
KAnalyze: A Fast Versatile Pipelined K-mer Toolkit.
Audano P1, Vannberg F.

VelvetK 20120606 – Find a reasonable K-mer size to Assemble Genome Reads with Velvet

VelvetK 20120606

:: DESCRIPTION

VelvetK can estimate the best k-mer size to use for your Velvet de novo assembly. It needs two inputs: the estimated genome size, and all your sequence read files. The genome size can be supplied as as a number (eg. 3.5M) or as a FASTA file of a closely related genome.

::DEVELOPER

Torsten Seemann

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 VelvetK

:: MORE INFORMATION

kPAL 2.1.1 – K-mer analysis toolkit and Programming Library

kPAL 2.1.1

:: DESCRIPTION

kPAL is an analysis toolkit and programming library for k-mer profiles.

::DEVELOPER

the Human Genetics department at Leiden University Medical Center.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Python

:: DOWNLOAD

  kPAL

:: MORE INFORMATION

Citation

Anvar et al.,
Determining the quality and complexity of next-generation sequencing data without a reference genome.
Genome Biology 2014, 15:555. doi:10.1186/s13059-014-0555-3

KCMBT – K-mer Counter based on Multiple Burst Trees

KCMBT

:: DESCRIPTION

KCMBT is a very fast multi-threaded k-mer counting algorithm. It uses cache efficient burst tries to store k-mers

::DEVELOPER

Abdullah-Al Mamun

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 KCMBT

:: MORE INFORMATION

Citation

KCMBT: A k-mer Counter based on Multiple Burst Trees.
Mamun AA, Pal S, Rajasekaran S.
Bioinformatics. 2016 Jun 9. pii: btw345.

2kplus2 0.1 – Find Single Nucleotide Polymorphisms in K-mer graphs

2kplus2 0.1

:: DESCRIPTION

2kplus2 is a new algorithm that search graphs produced from the de novo assembler cortex.

::DEVELOPER

Dan MacLean

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C ++ Compiler

:: DOWNLOAD

 2kplus2

:: MORE INFORMATION

Citation

Using 2k + 2 bubble searches to find Single Nucleotide Polymorphisms in k-mer graphs.
Younsi R, MacLean D.
Bioinformatics. 2014 Oct 24. pii: btu706.

UST – Compression of K-mers

UST

:: DESCRIPTION

UST is a bioinformatics tool for constructing a spectrum-preserving string set (SPSS) representation from sets of k-mers.

::DEVELOPER

Medvedev Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

UST

:: MORE INFORMATION

Citation:

Amatur Rahman and Paul Medvedev,
“Representation of k-mer sets using spectrum-preserving string sets”,
in submission.

ACE 1.01 – Accurate Correction of Errors using K-mer tries

ACE 1.01

:: DESCRIPTION

ACE corrects substitution errors in an Illumina archive using a k-mer trie.

::DEVELOPER

ACE team

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Linux  /MacOsX
  • C++

:: DOWNLOAD

  ACE

:: MORE INFORMATION

Citation

ACE: Accurate Correction of Errors using K-mer tries.
Sheikhizadeh S, de Ridder D.
Bioinformatics. 2015 May 28. pii: btv332.

findGSE – Estimating Genome Size Variation using k-mer Frequencies

findGSE

:: DESCRIPTION

findGSE is a tool for estimating size of (heterozygous diploid or homozygous) genomes by fitting k-mer frequencies iteratively with a skew normal distribution model.

::DEVELOPER

KS’ Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

findGSE

:: MORE INFORMATION

Citation

Bioinformatics. 2018 Feb 15;34(4):550-557. doi: 10.1093/bioinformatics/btx637.
findGSE: estimating genome size variation within human and Arabidopsis using k-mer frequencies.
Sun H, Ding J, Piednoël M, Schneeberger K.