Pybedtools: a flexible Python library for manipulating genomic datasets and annotations
نویسندگان
چکیده
SUMMARY pybedtools is a flexible Python software library for manipulating and exploring genomic datasets in many common formats. It provides an intuitive Python interface that extends upon the popular BEDTools genome arithmetic tools. The library is well documented and efficient, and allows researchers to quickly develop simple, yet powerful scripts that enable complex genomic analyses. AVAILABILITY pybedtools is maintained under the GPL license. Stable versions of pybedtools as well as documentation are available on the Python Package Index at http://pypi.python.org/pypi/pybedtools. CONTACT [email protected]; [email protected] SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
منابع مشابه
cyvcf2: fast, flexible variant analysis with Python
Motivation Variant call format (VCF) files document the genetic variation observed after DNA sequencing, alignment and variant calling of a sample cohort. Given the complexity of the VCF format as well as the diverse variant annotations and genotype metadata, there is a need for fast, flexible methods enabling intuitive analysis of the variant data within VCF and BCF files. Results We introdu...
متن کاملScribl: an HTML5 Canvas-based graphics library for visualizing genomic data over the web
MOTIVATION High-throughput biological research requires simultaneous visualization as well as analysis of genomic data, e.g. read alignments, variant calls and genomic annotations. Traditionally, such integrative analysis required desktop applications operating on locally stored data. Many current terabyte-size datasets generated by large public consortia projects, however, are already only fea...
متن کاملSequence analysis TRAL: tandem repeat annotation library
Motivation: Currently, more than 40 sequence tandem repeat detectors are published, providing heterogeneous, partly complementary, partly conflicting results. Results: We present TRAL, a tandem repeat annotation library that allows running and parsing of various detection outputs, clustering of redundant or overlapping annotations, several statistical frameworks for filtering false positive ann...
متن کاملA Python-Based Open Source System for Geographic Object-Based Image Analysis (GEOBIA) Utilizing Raster Attribute Tables
A modular system for performing Geographic Object-Based Image Analysis (GEOBIA), using entirely open source (General Public License compatible) software, is presented based around representing objects as raster clumps and storing attributes as a raster attribute table (RAT). The system utilizes a number of libraries, developed by the authors: The Remote Sensing and GIS Library (RSGISLib), the R...
متن کاملData management routines for reproducible research using the G-Node Python Client library
Structured, efficient, and secure storage of experimental data and associated meta-information constitutes one of the most pressing technical challenges in modern neuroscience, and does so particularly in electrophysiology. The German INCF Node aims to provide open-source solutions for this domain that support the scientific data management and analysis workflow, and thus facilitate future data...
متن کامل