PaPaRa 2.5 – PArsimony-based Phylogeny-Aware Read alignment program

PaPaRa 2.5

:: DESCRIPTION

PaPaRa is a PArsimony-based Phylogeny-Aware Read alignment program

::DEVELOPER

the Exelixis Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / WIndows
  • C Compier

:: DOWNLOAD

 PaPaRa

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2012 Aug 9;13:196. doi: 10.1186/1471-2105-13-196.
Coupling SIMD and SIMT architectures to boost performance of a phylogeny-aware alignment kernel.
Alachiotis N, Berger SA, Stamatakis A.

Trimmomatic 0.39 – A Flexible Read Trimming tool for Illumina NGS data

Trimmomatic 0.39

:: DESCRIPTION

Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and single ended data.The selection of trimming steps and their associated parameters are supplied on the command line.

::DEVELOPER

Usadel Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

  Trimmomatic

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Apr 28.
Trimmomatic: a flexible trimmer for Illumina sequence data.
Bolger AM1, Lohse M, Usadel B.

KARMA 0.9 – Aligner for Mapping Shotgun Sequencer FASTQ Read

KARMA 0.9

:: DESCRIPTION

Karma ( K-tuple Alignment with Rapid Matching Algorithm) is an index based high speed aligner for mapping shotgun sequencer FASTQ reads to a reference genome. Karma assembles FASTQ files from Solexa into a set of mapped reads using a genome reference. It does this by first creating a index of the genome reference, then uses portions of the read to index into the reference to find possible matches.

::DEVELOPER

Paul Anderson @ the Center for Statistical Genetics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 KARMA

:: MORE INFORMATION

ExomeCopy 1.16.0 – Copy Number Variant Detection from Exome Sequencing Read Depth

ExomeCopy 1.16.0

:: DESCRIPTION

ExomeCopy implements a hidden Markov model which uses positional covariates, such as background read depth and GC-content, to simultaneously normalize and segment the samples into regions of constant copy count.

::DEVELOPER

Department Computational Molecular Biology, Max-Planck-Institute for Molecular Genetics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • R package
  • BioConductor

:: DOWNLOAD

 ExomeCopy

:: MORE INFORMATION

Citation

Stat Appl Genet Mol Biol. 2011 Nov 8;10(1).
Modeling read counts for CNV detection in exome sequencing data.
Love MI, Myšičková A, Sun R, Kalscheuer V, Vingron M, Haas SA.

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.

CRAM toolkit 3.0 – Read and Write CRAM/BAM Files

CRAM toolkit 3.0

:: DESCRIPTION

The CRAM toolkit is a Java program for writing and reading CRAM files. The CRAM format, based on the research paper Efficient storage of high throughput DNA sequencing data using reference-based compression, will be described in detail in a separate specification. Briefly, the CRAM format is based on efficient compression of DNA sequences by storing only differences between aligned and reference sequences with provision for reads that do not map to the reference. The CRAM format is expected to dramatically lower the storage cost for archiving re-sequencing reads.

::DEVELOPER

The European Nucleotide Archive

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

  CRAM toolkit

:: MORE INFORMATION

Citation:

Genome Res. 2011 May;21(5):734-40. Epub 2011 Jan 18.
Efficient storage of high throughput DNA sequencing data using reference-based compression.
Hsi-Yang Fritz M, Leinonen R, Cochrane G, Birney E.

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.

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.

Phusion 2.1c – Assembly Genome Sequences from Whole Genome Shotgun(WGS) Reads

Phusion 2.1c

:: DESCRIPTION

Phusion is a software package for assembling genome sequences from whole genome shotgun(WGS) reads.

::DEVELOPER

Zemin Ning ( zn1@sanger.ac.uk ),Yong Gu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Phusion

:: MORE INFORMATION

Citation

The phusion assembler.
Mullikin JC and Ning Z
Genome research2003;13;1;81-90

NanoOK 0.62 – Alignment and Analysis of Nanopore Reads

NanoOK 0.62

:: DESCRIPTION

NanoOK is a tool from TGAC for alignment and analysis of Nanopore reads. NanoOK will extract reads as FASTA or FASTQ files, align them (with a choice of alignment tools), then generate a comprehensive multi-page PDF report containing yield, accuracy and quality analysis.

::DEVELOPER

The Genome Analysis Centre

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / VirtualBox
  • Java

:: DOWNLOAD

  NanoOK

:: MORE INFORMATION

Citation:

NanoOK: Multi-reference alignment analysis of nanopore sequencing data, quality and error profiles.
Leggett RM, Heavens D, Caccamo M, Clark MD, Davey RP.
Bioinformatics. 2015 Sep 17. pii: btv540