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.

KAT 2.4.2 – K-mer Analysis Toolkit

KAT 2.4.2

:: DESCRIPTION

KAT is a suite of tools that generate, analyse and compare k-mer spectra produced from sequence files.

::DEVELOPER

the Earlham Institute

:: SCREENSHOTS

N/a

:: REQUIREMENTS

:: DOWNLOAD

 KAT

:: MORE INFORMATION

Citation

Bioinformatics. 2017 Feb 15;33(4):574-576. doi: 10.1093/bioinformatics/btw663.
KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies.
Mapleson D, Garcia Accinelli G, Kettleborough G, Wright J, Clavijo BJ.

SeroBA 1.0.1 – k-mer based Pipeline to identify the Serotype from Illumina NGS reads

SeroBA 1.0.1

:: DESCRIPTION

SeroBA is a k-mer based Pipeline to identify the Serotype from Illumina NGS reads for given references.

::DEVELOPER

Pathogen Informatics, Wellcome Trust Sanger Institute

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

SeroBA

:: MORE INFORMATION

Citation

SeroBA: rapid high-throughput serotyping of Streptococcus pneumoniae from whole genome sequence data.
Epping L, van Tonder AJ, Gladstone RA, The Global Pneumococcal Sequencing Consortium, Bentley SD, Page AJ, Keane JA.
Microb Genom. 2018 Jul;4(7). doi: 10.1099/mgen.0.000186. Epub 2018 Jun 15.

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.

DSK 2.1.0 – K-mer Counting software

DSK 2.1.0

:: DESCRIPTION

DSK is a k-mer counting software, similar to Jellyfish. Jellyfish is very fast but limited to large-memory servers and k ≤ 32. In contrast, DSK supports large values of k, and runs with (almost-)arbitrarily low memory usage and reasonably low temporary disk usage. DSK can count k-mers of large Illumina datasets on laptops and desktop computers.

::DEVELOPER

Rayan CHIKHI

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 DSK

:: MORE INFORMATION

Citation

DSK: k-mer counting with very low memory usage.
Rizk G, Lavenier D, Chikhi R.
Bioinformatics. 2013 Mar 1;29(5):652-3. doi: 10.1093/bioinformatics/btt020. Epub 2013 Jan 16.

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

stringMLST – An ultrafast k-mer based MLST tool

stringMLST

:: DESCRIPTION

stringMLST is a tool for detecting the MLST of an isolate directly from the genome sequencing reads. stringMLST predicts the ST of an isolate in a completely assembly and alignment free manner.

::DEVELOPER

Jordan Lab

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 stringMLST

:: MORE INFORMATION

KmerGenie 1.6982 – K-mer size Selection for Genome Assembly

KmerGenie 1.6682

:: DESCRIPTION

KmerGenie estimates the best k-mer length for genome de novo assembly. Given a set of reads, KmerGenie first computes the k-mer abundance histogram for many values of k. Then, for each value of k, it predicts the number of distinct genomic k-mers in the dataset, and returns the k-mer length which maximizes this number. Experiments show that KmerGenie’s choices lead to assemblies that are close to the best possible over all k-mer lengths.

::DEVELOPER

Rayan Chikhi, Paul Medvedev

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows / MacOsX
  • R package
  • Python

:: DOWNLOAD

 KmerGenie

:: MORE INFORMATION

Citation:

Bioinformatics. 2014 Jan 1;30(1):31-7. doi: 10.1093/bioinformatics/btt310. Epub 2013 Jun 3.
Informed and automated k-mer size selection for genome assembly.
Chikhi R1, Medvedev P.