krocus 0.0.15 – Predict MLST directly from uncorrected long reads

krocus 0.0.15

:: DESCRIPTION

Krocus can predict a ST directly from uncorrected long reads, and which was designed to consume read data as it is produced, providing results in minutes.

::DEVELOPER

Pathogen Informatics, Wellcome Trust Sanger Institute

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

Krocus

:: MORE INFORMATION

Citation

PeerJ. 2018 Jul 31;6:e5233. doi: 10.7717/peerj.5233. eCollection 2018.
Rapid multi-locus sequence typing direct from uncorrected long reads using Krocus.
Page AJ, Keane JA.

NanoMark – DNA Assembly Benchmark for Nanopore long reads

NanoMark

:: DESCRIPTION

NanoMark is a system for benchmarking DNA assembly tools, based on 3rd generation sequencers.

::DEVELOPER

NanoMark team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 NanoMark

:: MORE INFORMATION

Citation

Evaluation of hybrid and non-hybrid methods for de novo assembly of nanopore reads.
Sović I, Križanović K, Skala K, Šikić M.
Bioinformatics. 2016 May 9. pii: btw237.

rHAT 0.1.1 – Fast Alignment of Noisy Long Reads with Regional Hashing

rHAT 0.1.1

:: DESCRIPTION

rHAT is a seed-and-extension-based noisy long read alignment tool. It is suitable for aligning 3rd generation sequencing reads which are in large read length with relatively high error rate, especially Pacbio’s Single Molecule Read-time (SMRT) sequencing reads.

::DEVELOPER

rHAT team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • C++ Compiler
:: DOWNLOAD

 rHAT

:: MORE INFORMATION

Citation

rHAT: fast alignment of noisy long reads with regional hashing.
Liu B, Guan D, Teng M, Wang Y.
Bioinformatics. 2015 Nov 14. pii: btv662.

BWA 0.7.12 – Burrows-Wheeler Aligner for Short and Long Reads.

BWA 0.7.12

:: DESCRIPTION

BWA (Burrows-Wheeler Aligner) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome. It implements two algorithms, bwa-short and BWA-SW. The former works for query sequences shorter than 200bp and the latter for longer sequences up to around 100kbp. Both algorithms do gapped alignment.

::DEVELOPER

BWA Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 BWA

:: MORE INFORMATION

Citation:

Li H. and Durbin R. (2009)
Fast and accurate short read alignment with Burrows-Wheeler Transform.
Bioinformatics, 25:1754-60.

FinisherSC 2.0 – A Repeat-aware tool for upgrading de-novo Assembly using Long Reads

FinisherSC 2.0

:: DESCRIPTION

FinisherSC is a repeat-aware and scalable tool for upgrading de-novo assembly using long reads.

::DEVELOPER

Ka-Kit Lam

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 FinisherSC 

:: MORE INFORMATION

Citation

FinisherSC : A repeat-aware tool for upgrading de-novo assembly using long reads.
Lam KK, LaButti K, Khalak A, Tse D.
Bioinformatics. 2015 Jun 3. pii: btv280.

AGILE 0.4.0 – AliGnIng Long rEads

AGILE 0.4.0

:: DESCRIPTION

AGILE is a sequence mapping tool specifically designed to map the longer reads (read length > 200) to a given reference genome. Currently it works for 454 reads, but efforts are being made to make it suitable to work for all sequencers, which produce longer reads. Looking at the current trend of increasing read lengths, soon most of the sequencers have read lengths > 200.

::DEVELOPER

Sanchit Misra

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 AGILE

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Jan 15;27(2):189-95. Epub 2010 Nov 18.
Anatomy of a hash-based long read sequence mapping algorithm for next generation DNA sequencing.
Misra S, Agrawal A, Liao WK, Choudhary A.