ngSeqUtils 1.2.1 – Utility Scripts in Python for Handling Next Generation Sequencing data

ngSeqUtils 1.2.1

:: DESCRIPTION

ngSeqUtils is a small collection of scripts to assist data analysis of Next Generation Sequencing data and handle wig, bigwig, and gff files in python.

::DEVELOPER

The Barton Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Python

:: DOWNLOAD

 ngSeqUtils

 :: MORE INFORMATION

cyvcf2 v0.11.5 – Fast, Flexible Variant Analysis with Python

cyvcf2 v0.11.5

:: DESCRIPTION

cyvcf2 is a Python library and software package for fast parsing and querying of VCF and BCF files and illustrate its speed, simplicity and utility.

::DEVELOPER

The Quinlan Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOs
  • Python

:: DOWNLOAD

cyvcf2

:: MORE INFORMATION

Citation:

Bioinformatics. 2017 Jun 15;33(12):1867-1869. doi: 10.1093/bioinformatics/btx057.
cyvcf2: fast, flexible variant analysis with Python.
Pedersen BS, Quinlan AR

Pybedtools 0.8.0 – Python extension to BEDTools

Pybedtools 0.8.0

:: DESCRIPTION

Pybedtools is a Python wrapper for Aaron Quinlan’s BEDtools and extends these “genome algebra” programs by offering feature-level manipulations from with Python.

::DEVELOPER

The Quinlan Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Python

:: DOWNLOAD

 Pybedtools

:: MORE INFORMATION

Citation:

Bioinformatics. 2011 Dec 15;27(24):3423-4. doi: 10.1093/bioinformatics/btr539
Pybedtools: a flexible Python library for manipulating genomic datasets and annotations.
Dale RK, Pedersen BS, Quinlan AR.

scikit-bio 0.5.5 – Python 3 package providing Data Structures, Algorithms and Educational Resources for Bioinformatics

scikit-bio 0.5.5

:: DESCRIPTION

scikit-bio is an open-source, BSD-licensed, python package providing data structures, algorithms, and educational resources for bioinformatics.

::DEVELOPER

Knight Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows /MacOsX
  • Python

:: DOWNLOAD

scikit-bio

:: MORE INFORMATION

ETE 3.1.1 – Python Environment for Phylogenetic Tree Exploration

ETE 3.1.1

:: DESCRIPTION

ETE (Environment for Tree Exploration ) is a python programming toolkit that assists in the automated manipulation, analysis and visualization of phylogenetic and other type of trees. It provides a wide range of tree handling methods, node annotation features, programmatic access to the phylomeDB database, and automatic orthology and paralogy prediction methods. In addition, an interactive tree visualization program, as well as a highly customizable tree drawing engine, is included.

::DEVELOPER

Gabaldón’s lab

:: SCREENSHOTS

N/A

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 ETE

:: MORE INFORMATION

Citation:

ETE 3: Reconstruction, analysis and visualization of phylogenomic data.
Huerta-Cepas J, Serra F, Bork P.
Mol Biol Evol. 2016 Feb 26. pii: msw046.

Jaime Huerta-Cepas*, Joaquín Dopazo and Toni Gabaldón*.
ETE: a python Environment for Tree Exploration.
BMC Bioinformatics 2010, 11:24.

Pydna 1.0.1 – Tool for DNA Assembly Strategies using Python

Pydna 1.0.1

:: DESCRIPTION

Pydna is an extensible, free and open source Python library for simulating basic molecular biology DNA unit operations such as restriction digestion, ligation, PCR, primer design, Gibson assembly and homologous recombination.

::DEVELOPER

Pydna team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/linux
  • Python

:: DOWNLOAD

  Pydna

:: MORE INFORMATION

Citation

Pydna: a simulation and documentation tool for DNA assembly strategies using python.
Pereira F, Azevedo F, Carvalho Â, Ribeiro GF, Budde MW, Johansson B.
BMC Bioinformatics. 2015 May 2;16(1):142.

Omics Integrator 0.2 – Python Scripts for Analyzing Diverse Forms of ‘omic’ data

Omics Integrator 0.2

:: DESCRIPTION

Omics Integrator is package comprised of command-line tools designed to integrate high-throughput datasets such as gene expression, phospho-proteomic data and the results from genetic screens.

::DEVELOPER

The Fraenkel Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

  Omics Integrator

:: MORE INFORMATION

Citation

Network-Based Interpretation of Diverse High-Throughput Datasets through the Omics Integrator Software Package.
Tuncbag N, Gosline SJ, Kedaigle A, Soltis AR, Gitter A, Fraenkel E.
PLoS Comput Biol. 2016 Apr 20;12(4):e1004879. doi: 10.1371/journal.pcbi.1004879

Illuminate 0.6.2 – Analytics toolkit in Python for Illumina HiSeq and MiSeq metrics

Illuminate 0.6.2

:: DESCRIPTION

Illuminate parses the metrics binaries that result from Illumina sequencer runs, and provides usable data in the form of python dictionaries and dataframes. Intended to emulate the output of Illumina SAV, illuminate allows you to print sequencing run metrics to the command line as well as work with the data programmatically.

::DEVELOPER

Naomi Most , InVitae

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ WIndows/MacOsX
  • Python

:: DOWNLOAD

 Illuminate

:: MORE INFORMATION

Biopython 1.66 – Tools for Biological Computation written in Python

Biopython 1.66

:: DESCRIPTION

Biopython is a set of freely available tools for biological computation written in Python by an international team of developers.It is a distributed collaborative effort to develop Python libraries and applications which address the needs of current and future work in bioinformatics.

::DEVELOPER

Biopython Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

Biopython

:: MORE INFORMATION

Citation:

Cock PJ, Antao T, Chang JT, Chapman BA, Cox CJ, Dalke A, Friedberg I, Hamelryck T, Kauff F, Wilczynski B, and de Hoon MJ.
Biopython: freely available Python tools for computational molecular biology and bioinformatics.
Bioinformatics 2009 Jun 1; 25(11) 1422-3. doi:10.1093/bioinformatics/btp163 pmid:19304878.

eSBMTools 1.04 – Python tools for enhanced Native Structure-based Modeling

eSBMTools 1.04

:: DESCRIPTION

eSBMTools: python tools that assist the setup and evaluation of native structure-based simulations of proteins and nucleic acids, both at the Cα and all-atom level. The tools interface with GROMACS and support its standard output formats. Information from other sources like bioinformatics or experimental data can be added to the standard native structure-based model (SBM).

::DEVELOPER

eSBMTools team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX/Windows
  • Python

:: DOWNLOAD

 eSBMTools

:: MORE INFORMATION

Citation:

Bioinformatics. 2013 Nov 1;29(21):2795-6. doi: 10.1093/bioinformatics/btt478. Epub 2013 Sep 9.
eSBMTools 1.0: enhanced native structure-based modeling tools.
Lutz B1, Sinner C, Heuermann G, Verma A, Schug A.