Tag: Shotgun

PatternLab for proteomics V – tool for analyzing Shotgun Proteomic data

PatternLab for proteomics V

:: 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

Laboratory for Computational and Strucutural Proteomics – Fiocruz

:: 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

WGSQuikr 1.0.0 – Whole-genome Shotgun Metagenomic Classification

WGSQuikr 1.0.0

:: DESCRIPTION

WGSQuikr is a very rapid, whole-genome shotgun metagenomic reconstruction.

::DEVELOPER

WGSQuikr team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX /Windows
  • MatLab

:: DOWNLOAD

 WGSQuikr

:: MORE INFORMATION

Citation

PLoS One. 2014 Mar 13;9(3):e91784. doi: 10.1371/journal.pone.0091784. eCollection 2014.
WGSQuikr: fast whole-genome shotgun metagenomic classification.
Koslicki D, Foucart S, Rosen G.

Philosopher 4.0.0 – Toolkit for Shotgun Proteomics data analysis

Philosopher 4.0.0

:: 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

Citation

da Veiga Leprevost F, Haynes SE, Avtonomov DM, Chang HY, Shanmugam AK, Mellacheruvu D, Kong AT, Nesvizhskii AI.
Philosopher: a versatile toolkit for shotgun proteomics data analysis.
Nat Methods. 2020 Sep;17(9):869-870. doi: 10.1038/s41592-020-0912-y. PMID: 32669682; PMCID: PMC7509848.

Celera Assembler 8.3 / Canu v2.2 – Whole Genome Shotgun Assembler

Celera Assembler 8.3 / Canu v2.2

:: 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

Canu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing (such as the PacBio RSII or Oxford Nanopore MinION).

::DEVELOPER

Celera Assembler team / Maryland Bioinformatics Labs (MarBL)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

Celera Assembler / Canu

:: MORE INFORMATION

Citation

Koren S, Walenz BP, Berlin K, Miller JR, Bergman NH, Phillippy AM.
Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation.
Genome Res. 2017 May;27(5):722-736. doi: 10.1101/gr.215087.116. Epub 2017 Mar 15. PMID: 28298431; PMCID: PMC5411767.

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

ProtMAX – Analyzing Large Shotgun Proteomics Mass Spectrometry data sets

ProtMAX

:: DESCRIPTION

ProtMAX is a fast and robust software tool for analyzing large shotgun proteomics mass spectrometry data sets.

::DEVELOPER

Molecular Systems Biology, University of Vienna

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 ProtMAX

:: MORE INFORMATION

Citation:

Nat Protoc. 2013 Mar;8(3):595-601. doi: 10.1038/nprot.2013.013. Epub 2013 Feb 28.
Using ProtMAX to create high-mass-accuracy precursor alignments from label-free quantitative mass spectrometry data generated in shotgun proteomics experiments.
Egelhofer V1, Hoehenwarter W, Lyon D, Weckwerth W, Wienkoop S.

AMOS 3.1.0 – Whole Genome Shotgun Assembler

AMOS 3.1.0

:: DESCRIPTION

AMOS (A Modular, Open-Source) consortium is committed to the development of open-source whole genome assembly software. The project acronym (AMOS) represents our primary goal — to produce A Modular, Open-Source whole genome assembler.Open-source so that everyone is welcome to contribute and help build outstanding assembly tools, and modular in nature so that new contributions can be easily inserted into an existing assembly pipeline. This modular design will foster the development of new assembly algorithms and allow the AMOS project to continually grow and improve in hopes of eventually becoming a widely accepted and deployed assembly infrastructure. In this sense, AMOS is both a design philosophy and a software system.

::DEVELOPER

AMOS Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

AMOS

:: MORE INFORMATION

Citation

Next generation sequence assembly with AMOS.
Treangen TJ, Sommer DD, Angly FE, Koren S, Pop M.
Curr Protoc Bioinformatics. 2011 Mar;Chapter 11:Unit 11.8. doi: 10.1002/0471250953.bi1108s33.

MIRA 4.9.6 – Whole Genome Shotgun and EST Sequence Assembler

MIRA 4.9.6

:: DESCRIPTION

MIRA (Mimicking Intelligent Read Assembly)is a whole genome shotgun and EST sequence assembler for Sanger, 454, Solexa (Illumina), IonTorrent data and PacBio (the later at the moment only CCS and error-corrected CLR reads). It can be seen as a Swiss army knife of sequence assembly developed and used in the past 12 years to get assembly jobs done efficiently – and especially accurately. That is, without actually putting too much manual work into finishing the assembly.

::DEVELOPER

Bastien Chevreux

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  Mac OsX

:: DOWNLOAD

 MIRA

:: MORE INFORMATION

Citation:

Chevreux et al. (2004)
Using the miraEST Assembler for Reliable and Automated mRNA Transcript Assembly and SNP Detection in Sequenced ESTs
Genome Research 2004. 14:1147-1159.

DISCOVAR 51750 – Genome Shotgun Assembler and Variant Caller

DISCOVAR 51750

:: DESCRIPTION

DISCOVAR is a whole genome shotgun assembler and variant caller that can generate high quality assemblies and variant calls from the latest 250 base Illumina PCR-free fragment reads.

::DEVELOPER

Computational Research and Development Group, Broad Institute of MIT and Harvard

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 DISCOVAR

:: MORE INFORMATION

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).

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.

Exit mobile version