Tag: Read

ExomeCopy 1.32.0 – Copy Number Variant Detection from Exome Sequencing Read Depth

ExomeCopy 1.32.0

:: 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.

BARCODE – A fast Lossless Read Compression tool based on Bloom Filters

BARCODE

:: DESCRIPTION

BARCODE achieves highly efficient compression by using a reference genome, but completely circumvents the need for alignment, affording a great reduction in the time needed to compress.

::DEVELOPER

Ron Shamir’s lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/ MacOsX
  • Python

:: DOWNLOAD

  BARCODE

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2014;15 Suppl 9:S7. doi: 10.1186/1471-2105-15-S9-S7. Epub 2014 Sep 10.
Fast lossless compression via cascading Bloom filters.
Rozov R, Shamir R, Halperin E.

bcm-ace-plots – Reads in an Ace format Assembly File produced by the Phrap

bcm-ace-plots

:: DESCRIPTION

bcm-ace-plots reads in an Ace format assembly file produced by the Phrap (Green et al.) assembly software. Using special tags in the read names, bcm-ace-plots will plot the template coverage, the template span, the coverage, the BAC coverage, the WGS coverage, quality, and high quality discrepancies.

::DEVELOPER

Human Genome Sequencing Center, Baylor College of Medicine

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux /  MacOsX
  • Java

:: DOWNLOAD

bcm-ace-plots

:: MORE INFORMATION

NanoOK 1.33 – Alignment and Analysis of Nanopore Reads

NanoOK 1.33

:: 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 Earlham Institute.

:: 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

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

PyroCleaner 1.3 – Clean 454 Pyrosequencing Reads in order to ease the Assembly Process

PyroCleaner 1.3

:: DESCRIPTION

The pyrocleaner is intended to clean the reads included in the sff file in order to ease the assembly process. It enables filtering sequences on different criteria such as length, complexity, number of undetermined bases which has been proven to correlate with poor quality and multiple copy reads. It also enables to clean paired-ends sff files and generates on one side a sff with the validated paired-ends and on the other the sequences which can be used as shotgun reads.

::DEVELOPER

the bioinformatic plateforms of Genotoul.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

  PyroCleaner

:: MORE INFORMATION

Citation

Mariette J, Noirot C, Klopp C.
Assessment of replicate bias in 454 pyrosequencing and a multi-purpose read-filtering tool.
BMC Research Notes 2011, 4:149

fastareader 0.1 – Read FASTA files in a Text or Binary Format

fastareader 0.1

:: DESCRIPTION

Fasta reader is designed to be helpful when reading in fasta files or when trying to index them in a smarter fashion for quick subsequence lookup. This library was mainly created for the second reason, but was meant to be compatible with also regular fasta text files for sub-sequence retrieval. It supports MFA in as far as it is possible.

::DEVELOPER

Misko Dzamba

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux / MacOsXJava

:: DOWNLOAD

 Fasta reader

:: MORE INFORMATION

AV454 1.0 – de novo Consensus Assembler designed for reads derived from diverse Viral Populations

AV454 1.0

:: DESCRIPTION

AV454 (AssembleViral454) is an assembler, based on the ARACHNE package, designed for small and non-repetitive genomes sequenced at high depth. It was specifically designed to assemble read data generated from a mixed population of viral genomes. Reads need not be paired, and it is assumed that no sequence repeat in the genome would be large enough to fully contain an average read.

::DEVELOPER

Computational R&D, The Broad Institute, Cambridge, MA

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 AV454

:: MORE INFORMATION