SUPER-FOCUS 0.34 – Agile Functional Analysis of Shotgun Metagenomic data

SUPER-FOCUS 0.34

:: 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.

Arachne 4.6233 – Whole-genome Shotgun Assembler

Arachne 4.6233

:: DESCRIPTION

ARACHNE is a program for assembling data from whole genome shotgun sequencing experiments. It was designed for long reads from Sanger sequencing technology, and has been used extensively to assemble many genomes, including many that are large and highly repetitive.

::DEVELOPER

Bonnie Berger 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

Arachne

:: MORE INFORMATION

Citation

Batzoglou S, Jaffe DB, Stanley K, Butler J, Gnerre S, Mauceli E, Berger B, Mesirov JP, Lander ES. 2002.
ARACHNE: a whole-genome shotgun assembler.
Genome Research12: 177–189.

Jaffe DB, Butler J, Gnerre S, Mauceli E, Lindblad-Toh K, Mesirov JP, Zody MC, Lander ES. 2003.
Whole-genome sequence assembly for mammalian genomes: Arachne 2.
Genome Research 13: 91–96.

Gnerre S, Lander ES, Lindblad-Toh K, Jaffe DB. 2009.
Assisted assembly: how to improve a de novo genome assembly by using related species.
Genome Biology10: R88.

PAnalyzer 1.1 – Protein Inference in Shotgun Proteomics

PAnalyzer 1.1

:: DESCRIPTION

PAnalyzer is a software tool focused on the protein inference process of shotgun proteomics.

::DEVELOPER

EhuBio

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX

:: DOWNLOAD

 PAnalyzer

:: MORE INFORMATION

Citation:

Prieto G, Aloria K, Osinalde N, Fullaondo A, Arizmendi JM, Matthiesen R:
PAnalyzer: A software tool for protein inference in shotgun proteomics.
BMC bioinformatics 2012, 13:288.

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

Ji Research Group

:: 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.

Philosopher 2.0.0 – Toolkit for Shotgun Proteomics data analysis

Philosopher 2.0.0

:: DESCRIPTION

Philosopher provides easy access to third-party tools and custom algorithms for proteomics analysis, from database searching to functional protein reports. Philosopher is also well-equipped for open search analysis, providing extended versions of PeptideProphet and ProteinProphet for peptide validation and protein inference.

::DEVELOPER

Proteomics & Integrative Bioinformatics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

Philosopher

:: MORE INFORMATION

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

ZhuLab, 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.

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

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.