ShotGun 1.0.10 – Flexible Short Read Simulator

ShotGun 1.0.10

:: DESCRIPTION

ShotGun is a flexible short read simulator. ShotGun generates sequence data with user-specified read length and average depth, accommodates to cycle specific sequencing error rates, allows the read depth distribution to be either the ideal Poisson or Negative Binomial to model the overdispersion observed with real sequencing data. In addition, ShotGun performs computationally efficient Single Nucleotide Polymorphism (SNP) discovery using a statistic aggregated across all sequenced samples. False positives can be controlled at any desired rate according to the null distribution of this multi-sample statistic.

::DEVELOPER

Yun Li Statistical Genetics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
:: DOWNLOAD

 ShotGun

:: MORE INFORMATION

SUPER-FOCUS 0.26 – Agile Functional Analysis of Shotgun Metagenomic data

SUPER-FOCUS 0.26

:: DESCRIPTION

SUPER-FOCUS (SUbsystems Profile by databasE Reduction using FOCUS) an agile homology-based approach using a reduced SEED database to report the subsystems present in metagenomic samples and profile their abundances.

::DEVELOPER

the Edwards Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Mac OsX / Linux
  • Python

:: DOWNLOAD

 SUPER-FOCUS

:: MORE INFORMATION

Citation:

SUPER-FOCUS: A tool for agile functional analysis of shotgun metagenomic data.
Silva GG, Green KT, Dutilh BE, Edwards RA.
Bioinformatics. 2015 Oct 9. pii: btv584.

MicrobeCensus 1.0.7 – Average Genome Size Estimation from Shotgun data

MicrobeCensus 1.0.7

:: DESCRIPTION

MicrobeCensus : Rapidly and accurate estimate the average genome size (AGS)

::DEVELOPER

Pollard Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 MicrobeCensus

:: MORE INFORMATION

Celera Assembler 8.3 – Whole Genome Shotgun Assembler

Celera Assembler 8.3

:: DESCRIPTION

Celera Assembler (wgs-assembler) is scientific software for DNA research. It can reconstruct long sequences of genomic DNA given the fragmentary data produced by whole-genome shotgun sequencing. The Celera Assembler has enabled discovery in microbial genomes, large eukaryotic genomes, diploid genomes, and genomes from environmental samples. Celera Assembler contributed the first diploid sequence of an individual human, and metagenomics assemblies of the Global Ocean Sampling

::DEVELOPER

Celera Genomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

Celera Assembler

:: MORE INFORMATION

Citation

Denisov et al. (2008)
Consensus Generation and Variant Detection by Celera Assembler.
Bioinformatics 24(8):1035-40

Perseus 1.5.2.6 – Shotgun Proteomics Data Analysis

Perseus 1.5.2.6

:: DESCRIPTION

is a software package for shotgun proteomics data analysis, which helps researchers to extract biologically meaningful information from their MaxQuant output such as posttranslational modifications.

::DEVELOPER

Jürgen Cox

:: SCREENSHOTS

Perseus

:: REQUIREMENTS

  • Windows 64bit
  • .NET Framework 4.5

:: DOWNLOAD

 Perseus

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2012;13 Suppl 16:S12. doi: 10.1186/1471-2105-13-S16-S12. Epub 2012 Nov 5.
1D and 2D annotation enrichment: a statistical method integrating quantitative proteomics with complementary high-throughput data.
Cox J, Mann M.

MAP 20121108 – A de novo Metagenomic Assembly program for Shotgun DNA reads

MAP 20121108

:: DESCRIPTION

MAP (Metagenomic Assembly program) is a de novo assembly approach and its implementation based on an improved Overlap/Layout/Consensus (OLC) strategy incorporated with several special algorithms.MAP uses the mate pair information, resulting in being more applicable to shotgun DNA reads (recommended as > 200 bp) currently widely-used in metagenome projects. Results of extensive tests on simulated data show that MAP can be superior to both Celera and Phrap for typical longer reads by Sanger sequencing, as well as has an evident advantage over Celera, Newbler, and the newest Genovo, for typical shorter reads by 454 sequencing.

::DEVELOPER

Medical information and systems biology laboratory, Peking Uiniversity, Beijing

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

MAP

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Jun 1;28(11):1455-62. Epub 2012 Apr 11.
A de novo metagenomic assembly program for shotgun DNA reads.
Lai B, Ding R, Li Y, Duan L, Zhu H.

MSAcquisitionSimulator 1.0.2 – Data-dependent Acquisition Simulator for LC-MS Shotgun Proteomics

MSAcquisitionSimulator 1.0.2

:: DESCRIPTION

MSAcquisitionSimulator is a collection of three command-line tools that simulate data-dependent acquisition algorithms on in silico generated ground truth data of liquid chromatography-mass spectrometry proteomics experiments.

::DEVELOPER

Major Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

MSAcquisitionSimulator

:: MORE INFORMATION

Citation

MSAcquisitionSimulator: data-dependent acquisition simulator for LC-MS shotgun proteomics.
Goldfarb D, Wang W, Major MB.
Bioinformatics. 2015 Dec 17. pii: btv745.

PatternLab for proteomics 4.0.0.7 – tool for analyzing Shotgun Proteomic data

PatternLab for proteomics 4.0.0.7

:: DESCRIPTION

PatternLab for proteomics is a one-stop shop computational environment for analyzing shotgun proteomic data. Its modules provide means to pinpoint proteins/peptides that are differentially expressed and those that are unique to a state. It can also cluster the ones that share similar expression profiles in time-course experiments, as well as help in interpreting results according to Gene Ontology.

::DEVELOPER

Paulo Costa Carvalho

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 PatternLab for proteomics

:: MORE INFORMATION

Citation

Paulo C. Carvalho, John R. Yates III, Valmir C. Barbosa
Analyzing Shotgun Proteomic Data with PatternLab for Proteomics
Current Protocols in Bioinformatics Unit 13.13 DOI: 10.1002/0471250953.bi1313s30

GRAMMy – Shotgun Metagenomics Analysis

GRAMMy

:: DESCRIPTION

GRAMMy is a computational framework developed for Genome Relative Abundance using Mixture Model theory (GRAMMy) based estimation. Accurate estimation of microbial community composition based on metagenomic sequencing data is fundamental for metagenomics analysis. Prevalent estimation methods are mainly based on directly summarizing alignment results or its variants; often result in biased and/or unstable estimates.

::DEVELOPER

Fengzhu Sun

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • Python

:: DOWNLOAD

 GRAMMy

:: MORE INFORMATION

Citation

PLoS One. 2011;6(12):e27992. doi: 10.1371/journal.pone.0027992. Epub 2011 Dec 6.
Accurate genome relative abundance estimation based on shotgun metagenomic reads.
Xia LC1, Cram JA, Chen T, Fuhrman JA, Sun F.

ALLPATHS-LG 51750 – Whole Genome Shotgun Assembler

ALLPATHS-LG 51750

:: DESCRIPTION

ALLPATHS-LG (Large Genome) is a whole genome shotgun assembler that can generate high quality assemblies from short reads. It works on both small and large (mammalian size) genomes. To use it, you should first generate ~100 base Illumina reads from two libraries: one from ~180 bp fragments, and one from ~3000 bp fragments, both at about 45x coverage. Sequence from longer fragments will enable longer-range continuity.

::DEVELOPER

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

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

ALLPATHS-LG

:: MORE INFORMATION

Citation

Gnerre S, MacCallum I, Przybylski D, Ribeiro F, Burton J, Walker B, Sharpe T, Hall G, Shea T, Sykes S, Berlin A, Aird D, Costello M, Daza R, Williams L, Nicol R, Gnirke A, Nusbaum C, Lander ES, Jaffe DB. 2010.
High-quality draft assemblies of mammalian genomes from massively parallel sequence data.
Proceedings of the National Academy of Sciences USA (epub ahead of print, Dec. 27, 2010).