Tag: Read

misFinder v0.4.05.05 – Identify Mis-assemblies in an unbiased manner using Reference and Paired-end Reads

misFinder v0.4.05.05

:: DESCRIPTION

misFinder is a tool that aims to identify the assembly errors with high accuracy in an unbiased way and correct these errors at their mis-assembled positions to improve the assembly accuracy for downstream analysis.

::DEVELOPER

misFinder team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 misFinder

:: MORE INFORMATION

Citation

misFinder: identify mis-assemblies in an unbiased manner using reference and paired-end reads.
Zhu X, Leung HC, Wang R, Chin FY, Yiu SM, Quan G, Li Y, Zhang R, Jiang Q, Liu B, Dong Y, Zhou G, Wang Y.
BMC Bioinformatics. 2015 Nov 16;16(1):386.

Coral 1.4.1 – Error Correction Algorithm for Correcting reads from DNA sequencing platforms

Coral 1.4.1

:: DESCRIPTION

Coral is an error correction algorithm for correcting reads from DNA sequencing platforms such as the Illumina Genome Analyzer or HiSeq platforms or Roche/454 Genome Sequencer. Coral can utilize also bases distant from the error in the correction process because the whole read is present in the alignment. Coral is easily adjustable to reads produced by different sequencing technologies like Illumina Genome Analyzer and Roche/454 Life Sciences sequencing platforms because the sequencing error model can be defined by the user.

::DEVELOPER

Jan Schröder , Leena Salmela

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Coral

:: MORE INFORMATION

Citation:

Bioinformatics. 2011 Jun 1;27(11):1455-61. Epub 2011 Apr 5.
Correcting errors in short reads by multiple alignments.
Salmela L, Schröder J.

Parseq rev02 – Infer Transcription level from RNA-Seq Read Counts

Parseq rev02

:: DESCRIPTION

Parseq is a statistical approach for transcription landscape reconstruction at a basepair resolution from RNA Seq read counts.

::DEVELOPER

Laboratory of Computational and Quantitative Biology(LCQB)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Parseq

:: MORE INFORMATION

Citation

Bioinformatics. 2014 May 15;30(10):1409-16. doi: 10.1093/bioinformatics/btu042. Epub 2014 Jan 27.
Parseq: reconstruction of microbial transcription landscape from RNA-Seq read counts using state-space models.
Mirauta B1, Nicolas P, Richard H.

InfoTrim – DNA Read Quality Trimmer using Entropy Created with Python

InfoTrim

:: DESCRIPTION

InfoTrim is a DNA read quality trimmer based on the Trimmomatic maximum information criterion model.

::DEVELOPER

Professor Zhang Liqing’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

InfoTrim

:: MORE INFORMATION

Citation

InfoTrim: A DNA read quality trimmer using entropy
2017 IEEE 7th International Conference on Computational Advances in Bio and Medical Sciences (ICCABS)

XS v2 – FASTQ Read Simulator

XS v2

:: DESCRIPTION

XS (eXtra Small)is a skilled FASTQ read simulation tool, flexible, portable (does not need a reference sequence) and tunable in terms of sequence complexity.

::DEVELOPER

UA.PT Bioinformatics

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux

:: DOWNLOAD

 XS

:: MORE INFORMATION

Citation

BMC Res Notes. 2014 Jan 16;7:40. doi: 10.1186/1756-0500-7-40.
XS: a FASTQ read simulator.
Pratas D1, Pinho AJ, Rodrigues JM.

Arioc 1.43 – High-throughput Read Alignment with GPU-accelerated Exploration of Seed-and-extend Search Space

Arioc 1.43

:: DESCRIPTION

Arioc is a set of computer programs that carry out the alignment of short DNA sequences to a comparatively large reference sequence or genome.

::DEVELOPER

Arioc team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows

:: DOWNLOAD

 Arioc

:: MORE INFORMATION

Citation

Arioc: high-throughput read alignment with GPU-accelerated exploration of the seed-and-extend search space.
Wilton R, Budavari T, Langmead B, Wheelan SJ, Salzberg SL, Szalay AS.
PeerJ. 2015 Mar 3;3:e808. doi: 10.7717/peerj.808. eCollection 2015.

ROVER 2.0.0 / UNDR ROVER 2.0.0 – Read Overlap Variant Caller

ROVER 2.0.0 / UNDR ROVER 2.0.0

:: DESCRIPTION

ROVER is a read-pair overlap considerate variant-calling software for PCR-based massively parallel sequencing datasets

UNDR ROVER (Unmapped Primer directed read overlap Variant caller) is an improved version of our ROVER variant calling tool for targeted DNA sequencing.

::DEVELOPER

Bernie Pope

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • Python

:: DOWNLOAD

 ROVER , UNDR ROVER

:: MORE INFORMATION

Citation:

UNDR ROVER – a fast and accurate variant caller for targeted DNA sequencing.
Park DJ, Li R, Lau E, Georgeson P, Nguyen-Dumont T, Pope BJ.
BMC Bioinformatics. 2016 Apr 16;17(1):165. doi: 10.1186/s12859-016-1014-9.

ROVER variant caller: read-pair overlap considerate variant-calling software applied to PCR-based massively parallel sequencing datasets.
Pope BJ, Nguyen-Dumont T, Hammet F, Park DJ.
Source Code Biol Med. 2014 Jan 24;9(1):3. doi: 10.1186/1751-0473-9-3.

IsoCon 0.3.2 – Deriving Finished Transcript Sequences from Iso-Seq reads

IsoCon 0.3.2

:: DESCRIPTION

IsoCon is a tool for reconstructing highly similar sequences present in a dataset of from long noisy reads

::DEVELOPER

Medvedev Group

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux / MacOsX
  • Python

:: DOWNLOAD

IsoCon

:: MORE INFORMATION

Citation

Kristoffer Sahlin, Marta Tomaszkiewicz, Kateryna D. Makova, Paul Medvedev
Deciphering highly similar multigene family transcripts from iso-seq data with isocon.
Nature Communications, 9(1):4601, 2018

scarpa 0.241 – Scaffolding Reads with Practical Algorithms

scarpa 0.241

:: DESCRIPTION

Scarpa is a stand-alone scaffolding tool for NGS data. It can be used together with virtually any genome assembler and any NGS read mapper that supports SAM format. Other features include support for multiple libraries and an option to estimate insert size distributions from data.

::DEVELOPER

Nilgun Donmez and Michael Brudno

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 scarpa

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Feb 15;29(4):428-34. doi: 10.1093/bioinformatics/bts716. Epub 2012 Dec 29.
SCARPA: scaffolding reads with practical algorithms.
Donmez N, Brudno M.

CORA 1.1.5b – compressive-acceleration tool for NGS Read Mapping methods

CORA 1.1.5b

:: DESCRIPTION

CORA is a compressive-acceleration tool for NGS read mapping methods. When plugged into existing mapping tools, CORA achieves substantial runtime improvement through the use of compressive representation of the reads and a comprehensive homology map of the reference genome.

::DEVELOPER

Bonnie Berger 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

CORA

:: MORE INFORMATION

Citation:

Deniz Yorukoglu, Y. William Yu, Jian Peng, Bonnie Berger.
Compressive Mapping for Next-generation Sequencing
Nature Biotechnology 34, 374-376 (2016) doi:10.1038/nbt.3511.

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