Kontaminant – Kmer-based Screening and Filtering tool for Next-gen Sequencing Reads

Kontaminant

:: DESCRIPTION

Kontaminant is a kmer-based screening and filtering tool for next-gen sequencing reads.

::DEVELOPER

the Earlham Institute.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 Kontaminant

:: MORE INFORMATION

Citation

Host Subtraction, Filtering and Assembly Validations for Novel Viral Discovery Using Next Generation Sequencing Data.
Daly, G.M., Leggett, R.M., Rowe, W., Stubbs, S., Wilkinson, M., Ramirez-Gonzalez, R.H., Caccamo, M., Bernal, W., Heeney, J.L.
PLoS One. 2015 Jun 22;10(6):e0129059. doi: 10.1371/journal.pone.0129059

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

miRNA-deKmer – Identification of microRNA precursor with the degenerate K-tuple or Kmer strategy

miRNA-deKmer

:: DESCRIPTION

miRNA-deKmer is a web server of identification of microRNA precursor with the degenerate K-tuple or Kmer strategy.

::DEVELOPER

Liu Lab, Harbin Institute of Technology Shenzhen Graduate School.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Identification of microRNA precursor with the degenerate K-tuple or Kmer strategy.
Liu B, Fang L, Wang S, Wang X, Li H, Chou KC.
J Theor Biol. 2015 Nov 21;385:153-9. doi: 10.1016/j.jtbi.2015.08.025.

KmerStream 1.0 – Computing kmer statistics for massive Genomics Datasets

KmerStream 1.0

:: DESCRIPTION

KmerStream is a streaming algorithm for estimating the number of distinct k-mers present in high throughput sequencing data.

::DEVELOPER

Pall Melsted

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • C++ COmpiler

:: DOWNLOAD

 KmerStream

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Oct 28. pii: btu713.
KmerStream: Streaming algorithms for k-mer abundance estimation.
Melsted P, Halldórsson BV

k-mer Tools 20110322 – Variety of Analysis based on Kmers

k-mer Tools 20110322

:: DESCRIPTION

kmer Tools is a suite of tools for DNA sequence analysis. It provides tools for searching (ESTs, mRNAs, sequencing reads); aligning (ESTs, mRNAs, whole genomes); and a variety of analyses based on kmers.

::DEVELOPER

J. Craig Venter Institute

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

k-mer Tools

:: MORE INFORMATION

N/A