fgbio

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.

• Goals
• Overview
• List of tools
• Building
• Command line
• Include fgbio in your project
• Contributing
• Authors
• License
• Sponsorship

Goals

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:

• Robust, well-tested tools.
• An easy to use command-line.
• Clear and thorough documentation for each tool.
• Open source development for the benefit of the community and our clients.

Overview

Fgbio is a set of command line tools to perform bioinformatic/genomic data analysis. The collection of tools within

fgbio

List of 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.

• Tools for working with Unique Molecular Indexes (UMIs, aka Molecular IDs or MIDs).
  • Annotating/Extract Umis from read-level data:

    AnnotateBamWithUmis

    and

    ExtractUmisFromBam

    .
  • Tools to manipulate read-level data containing Umis:

    CorrectUmis

    ,

    GroupReadsByUmi

    ,

    CallMolecularConsensusReads

    and

    CallDuplexConsensusReads

• Tools to manipulate read-level data:
  • FastqManipulation:

    DemuxFastqs

    and

    FastqToBam

  • Filter read-level data:

    FilterBam

    .
  • Clipping of reads:

    ClipBam

    .
  • Randomize the order of read-level data:

    RandomizeBam

    .
  • Update read-level metadata:

    SetMateInformation

    and

    UpdateReadGroups

    .
• Quality assessment tools:
  • Detailed substitution error rate evaluation:

    ErrorRateByReadPosition

  • Sample pooling QC:

    EstimatePoolingFractions

  • Splice-aware insert size QC for RNA-seq libraries:

    EstimateRnaSeqInsertSize

  • Assessment of duplex sequencing experiments:

    CollectDuplexSeqMetrics

• Miscellaneous tools:
  • Pick molecular indices (ex. sample barcodes, or molecular indexes):

    PickIlluminaIndices

    and

    PickLongIndices

    .
  • Convert the output of HAPCUT (a tool for phasing variants):

    HapCutToVcf

    .
  • Find technical or synthetic sequences in read-level data:

    FindTechnicalReads

    .
  • Assess phased variant calls:

    AssessPhasing

    .

Building

Cloning the Repository

Git LFS is used to store large files used in testing fgbio. In order to compile and run tests it is necessary to install git lfs. To retrieve the large files either:

1. Clone the repository after installing git lfs, or
2. In a previously cloned repository run

   git lfs pull

   once

After initial setup regular git commands (e.g.

pull

fetch

push

To clone the repository:

git clone https://github.com/fulcrumgenomics/fgbio.git

Running the build

fgbio is built using sbt.

Use

sbt assembly

target/scala-2.13/

Tests may be run with

sbt test

Java SE 8 is required.

Command line

java -jar target/scala-2.13/fgbio-.jar

java -jar target/scala-2.13/fgbio-.jar 

Include fgbio in your project

You can include

fgbio

"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.

Contributing

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.

Authors

• Tim Fennell (maintainer)
• Nils Homer (maintainer)

License

fgbio

Sponsorship

Become a sponsor

As a free and open source project,

fgbio

fgbio

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Sponsors

Sponsors provide support for

fgbio

The full list of sponsors supporting

fgbio