fgbio

by fulcrumgenomics

fulcrumgenomics / fgbio

Tools for working with genomic and high throughput sequencing data.

141 Stars 24 Forks Last release: about 2 months ago (1.3.0) MIT License 557 Commits 19 Releases

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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

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
are 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

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
) will also operate on large files and no special handling is needed.

To clone the repository:

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

Running the build

fgbio is built using sbt.

Use

sbt assembly
to build an executable jar in
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
to see the commands supported. Use
java -jar target/scala-2.13/fgbio-.jar 
to see the help message for a particular command.

Include fgbio in your project

You can include

fgbio
in 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.

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

License

fgbio
is open source software released under the MIT License.

Sponsorship

Become a sponsor

As a free and open source project,

fgbio
relies 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

Sponsors provide support for

fgbio
through direct funding or employing contributors. Public sponsors include:

Fulcrum Genomics   TwinStrand Biosciences   Jumpcode Genomics   iGenomX   Myriad Genetics   Mission Bio   Singular Genomics   Verogen   Integrated DNA Technologies   Strata Oncology

The full list of sponsors supporting

fgbio
is available in the sponsor page.

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