fulcrumgenomics/fgbio

How fulcrumgenomics/fgbio works

fgbio is a command-line toolkit for genomic and next-generation sequencing analysis. Users invoke focused tools on read-level or variant-level data; capabilities include FASTQ processing and demultiplexing, BAM manipulation, UMI consensus workflows, reference-file utilities, variant operations, and quality-control metrics. The graph groups these product areas and includes the shared command-line and SAM/BAM foundations. The README documents the tool capabilities and broad input types; sampled source excerpts are incomplete, so internal links between individual tools are omitted where their calls are not shown.

Main entry points: FgBioMain.scala Tool commands · DemuxFastqs.scala FASTQ tools · FilterBam.scala BAM tools · AnnotateBamWithUmis.scala UMI annotation

Components 24

Command line

Tool commands src/main/scala/com/fulcrumgenomics/cmdline/FgBioMain.scala
Tool API src/main/scala/com/fulcrumgenomics/cmdline/FgBioTool.scala
Shared definitions src/main/scala/com/fulcrumgenomics/FgBioDef.scala

Read processing

FASTQ tools src/main/scala/com/fulcrumgenomics/fastq/DemuxFastqs.scala
FASTQ I/O src/main/scala/com/fulcrumgenomics/fastq/FastqSource.scala
BAM tools src/main/scala/com/fulcrumgenomics/bam/FilterBam.scala
BAM utilities src/main/scala/com/fulcrumgenomics/bam/Bams.scala
SAM reader src/main/scala/com/fulcrumgenomics/bam/api/SamSource.scala
SAM records src/main/scala/com/fulcrumgenomics/bam/api/SamRecord.scala
SAM writer src/main/scala/com/fulcrumgenomics/bam/api/SamWriter.scala
Sample metadata src/main/scala/com/fulcrumgenomics/illumina/Sample.scala

UMI workflows

UMI annotation src/main/scala/com/fulcrumgenomics/umi/AnnotateBamWithUmis.scala
UMI grouping src/main/scala/com/fulcrumgenomics/umi/GroupReadsByUmi.scala
Consensus reads src/main/scala/com/fulcrumgenomics/umi/CallMolecularConsensusReads.scala
Consensus tags src/main/scala/com/fulcrumgenomics/umi/ConsensusTags.scala

Reference and variants

FASTA tools src/main/scala/com/fulcrumgenomics/fasta/UpdateFastaContigNames.scala
Sequence dictionary src/main/scala/com/fulcrumgenomics/fasta/SequenceDictionary.scala
VCF tools src/main/scala/com/fulcrumgenomics/vcf/MakeMixtureVcf.scala
Variant model src/main/scala/com/fulcrumgenomics/vcf/api/Variant.scala

Quality control

Read QC src/main/scala/com/fulcrumgenomics/bam/ErrorRateByReadPosition.scala
RNA-seq QC src/main/scala/com/fulcrumgenomics/rnaseq/EstimateRnaSeqInsertSize.scala
Metrics src/main/scala/com/fulcrumgenomics/util/Metric.scala

Other components

Bioinformatics user
FASTQ / BAM inputs

Connections 12

Bioinformatics user → Tool commands: runs README.md
Tool commands → FASTQ tools: runs README.md
Tool commands → BAM tools: runs README.md
Tool commands → UMI annotation: runs README.md
Tool commands → UMI grouping: runs README.md
Tool commands → Consensus reads: runs README.md
Tool commands → FASTA tools: runs README.md
Tool commands → VCF tools: runs README.md
Tool commands → Read QC: runs README.md
Tool commands → RNA-seq QC: runs README.md
FASTQ / BAM inputs → FASTQ tools: provides reads README.md
FASTQ / BAM inputs → BAM tools: provides reads README.md

Drawn by GitDiagram on November 9, 2026 from the repository's file tree, README and source files. Read as Markdown ·