Tools for working with genomic and high throughput sequencing data.
A set of tools to analyze genomic data with a focus on Next Generation Sequencing. This readme document is mostly for developers/contributors and those attempting to build the project from source. Detailed user documentation is available on the project website including tool usage and documentation of metrics produced. Detailed developer documentation can be found here.
There are many toolkits available for analyzing genomic data; fgbio does not aim to be all things to all people but is specifically focused on providing:
Fgbio is a set of command line tools to perform bioinformatic/genomic data analysis. The collection of tools within
fgbioare used by our customers and others both for ad-hoc data analysis and within production pipelines. These tools typically operate on read-level data (ex. FASTQ, SAM, or BAM) or variant-level data (ex. VCF or BCF). They range from simple tools to filter reads in a BAM file, to tools to compute consensus reads from reads with the same molecular index/tag. See the list of tools for more detail on the tools
For a full list of available tools please see the tools section of the project website.
Below we highlight a few tools that you may find useful.
git lfs pullonce
After initial setup regular git commands (e.g.
push) will also operate on large files and no special handling is needed.
To clone the repository:
git clone https://github.com/fulcrumgenomics/fgbio.git
fgbio is built using sbt.
sbt assemblyto build an executable jar in
Tests may be run with
Java SE 8 is required.
java -jar target/scala-2.13/fgbio-.jarto see the commands supported. Use
java -jar target/scala-2.13/fgbio-.jarto see the help message for a particular command.
You can include
fgbioin your project using:
"com.fulcrumgenomics" %% "fgbio" % "1.0.0"
for the latest released version or (buyer beware):
"com.fulcrumgenomics" %% "fgbio" % "0.9.0--SNAPSHOT"
for the latest development snapshot.
Contributions are welcome and encouraged. We will do our best to provide an initial response to any pull request or issue within one-week. For urgent matters, please contact us directly.
fgbiois open source software released under the MIT License.
As a free and open source project,
fgbiorelies on the support of the community of users for its development. If you work for an organization that uses and benefits from
fgbio, please consider supporting
fgbio. There are different ways, such as employing people to work on
fgbio, funding the project, or becoming a sponsor to support the broader ecosystem. Please [email protected] to discuss.
Sponsors provide support for
fgbiothrough direct funding or employing contributors. Public sponsors include:
The full list of sponsors supporting
fgbiois available in the sponsor page.