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Improve the list of tools in the README.md #991

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Improve the list of tools in the README.md #991

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Improve the list of tools in the README.md
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Expand Up @@ -67,25 +67,60 @@ For a full list of available tools please see the [tools section](http://fulcrum

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`.
- Tools for working with Unique Molecular Indexes (UMIs, aka Molecular IDs or Molecular Barcodes):
- Annotating/Extract Umis from read-level data: [`FastqToBam`][fgbio-fastqtobam-link], [`AnnotateBamWithUmis`][fgbio-annotatebamwithumis-link], [`ExtractUmisFromBam`][fgbio-extractumisfrombam-link], and [`CopyUmiFromReadName`][fgbio-copyumifromreadname-link].
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- Manipulate read-level data containing Umis: [`CorrectUmis`][fgbio-correctumis-link], [`GroupReadsByUmi`][fgbio-groupreadsbyumi-link], [`CallMolecularConsensusReads`][fgbio-callmolecularconsensusreads-link], [`CallDuplexConsensusReads`][fgbio-callduplexconsensusreads-link], and [`FilterConsensusReads`][fgbio-filterconsensusreads-link].
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- Tools for working with Unique Molecular Indexes (UMIs, aka Molecular IDs or Molecular Barcodes):
- Annotating/Extract Umis from read-level data: [`FastqToBam`][fgbio-fastqtobam-link], [`AnnotateBamWithUmis`][fgbio-annotatebamwithumis-link], [`ExtractUmisFromBam`][fgbio-extractumisfrombam-link], and [`CopyUmiFromReadName`][fgbio-copyumifromreadname-link].
- Manipulate read-level data containing Umis: [`CorrectUmis`][fgbio-correctumis-link], [`GroupReadsByUmi`][fgbio-groupreadsbyumi-link], [`CallMolecularConsensusReads`][fgbio-callmolecularconsensusreads-link], [`CallDuplexConsensusReads`][fgbio-callduplexconsensusreads-link], and [`FilterConsensusReads`][fgbio-filterconsensusreads-link].
- Tools for working with Unique Molecular Indexes (UMIs, aka Molecular IDs or Molecular Barcodes):
- Annotating/Extract UMIs from read-level data: [`FastqToBam`][fgbio-fastqtobam-link], [`AnnotateBamWithUmis`][fgbio-annotatebamwithumis-link], [`ExtractUmisFromBam`][fgbio-extractumisfrombam-link], and [`CopyUmiFromReadName`][fgbio-copyumifromreadname-link].
- Manipulate read-level data containing UMIs: [`CorrectUmis`][fgbio-correctumis-link], [`GroupReadsByUmi`][fgbio-groupreadsbyumi-link], [`CallMolecularConsensusReads`][fgbio-callmolecularconsensusreads-link], [`CallDuplexConsensusReads`][fgbio-callduplexconsensusreads-link], and [`FilterConsensusReads`][fgbio-filterconsensusreads-link].

Although UMI gets title cased in the tool names, I think it should be all caps in the docs (since it's an acronym)

- Collect metrics and review consensus reads: [`CollectDuplexSeqMetrics`][fgbio-collectduplexseqmetrics-link] and [`ReviewConsensusVariants`][fgbio-reviewconsensusvariants-link].
- Tools to manipulate read-level data:
- Fastq Manipulation: [`FastqToBam`][fgbio-fastqtobam-link], [`ZipperBams`][fgbio-zipperbams-link], and [`DemuxFastqs`][fgbio-demuxfastqs-link] (see `[fqtk`][fqtk-link], our rust re-implementation for sample demultiplexing).
- Filter, clip, randomize, sort, and update metadata for read-level data: [`FilterBam`][fgbio-filterbam-link], [`ClipBam`][fgbio-clipbam-link], [`RandomizeBam`][fgbio-randomizebam-link], [`SortBam`][fgbio-sortbam-link], [`SetMateInformation`][fgbio-setmateinformation-link] and [`UpdateReadGroups`][fgbio-updatereadgroups-link].
- Tools for quality control assessment:
- Detailed substitution error rate evaluation: [`ErrorRateByReadPosition`][fgbio-errorratebyreadposition-link].
- Sample pooling QC: [`EstimatePoolingFractions`]: [fgbio-estimatepoolingfractions-link].
- Splice-aware insert size QC for RNA-seq libraries: [`EstimateRnaSeqInsertSize`][fgbio-estimaternaseqinsertsize-link].
- Tools for adding or manipulating alternate contig names:
- Extract from a NCBI Assembly Report: [`CollectAlternateContigNames`][fgbio-collectalternatecontignames-link].
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- Update contig names in common file formats: [`UpdateFastaContigNames`][fgbio-updatefastacontignames-link], [`UpdateVcfContigNames`][fgbio-updatevcfcontignames-link], [`UpdateGffContigNames`][fgbio-updategffcontignames-link], [`UpdateIntervalListContigNames`][fgbio-updateintervallistcontignames-link], [`UpdateDelimitedFileContigNames`][fgbio-updatedelimitedfilecontignames-link].
- Miscellaneous tools:
- Pick molecular indices (ex. sample barcodes, or molecular indexes): [`PickIlluminaIndices`][fgbio-pickilluminaindices-link] and [`PickLongIndices`][fgbio-picklongindices-link].
- Find technical/synthetic, or switch-back sequences in read-level data: [`FindTechnicalReads`][fgbio-findtechnicalreads-link] and [`FindSwitchbackReads`][fgbio-findswitchbackreads-link].
- Make synthetic mixture VCFs: [`MakeMixtureVcf`][fgbio-makemixturevcf-link] and [`MakeTwoSampleMixtureVcf`][fgbio-maketwosamplemixturevcf-link].

[fgbio-fastqtobam-link]: https://fulcrumgenomics.github.io/fgbio/tools/latest/FastqToBam.html
[fgbio-annotatebamwithumis-link]: https://fulcrumgenomics.github.io/fgbio/tools/latest/AnnotateBamWithUmis.html
[fgbio-extractumisfrombam-link]: https://fulcrumgenomics.github.io/fgbio/tools/latest/ExtractUmisFromBam.html
[fgbio-copyumifromreadname-link]: https://fulcrumgenomics.github.io/fgbio/tools/latest/CopyUmiFromReadName.html
[fgbio-correctumis-link]: https://fulcrumgenomics.github.io/fgbio/tools/latest/CorrectUmis.html
[fgbio-groupreadsbyumi-link]: https://fulcrumgenomics.github.io/fgbio/tools/latest/GroupReadsByUmi.html
[fgbio-callmolecularconsensusreads-link]: https://fulcrumgenomics.github.io/fgbio/tools/latest/CallMolecularConsensusReads.html
[fgbio-callduplexconsensusreads-link]: https://fulcrumgenomics.github.io/fgbio/tools/latest/CallDuplexConsensusReads.html
[fgbio-filterconsensusreads-link]: https://fulcrumgenomics.github.io/fgbio/tools/latest/FilterConsensusReads.html
[fgbio-collectduplexseqmetrics-link]: https://fulcrumgenomics.github.io/fgbio/tools/latest/CollectDuplexSeqMetrics.html
[fgbio-reviewconsensusvariants-link]: https://fulcrumgenomics.github.io/fgbio/tools/latest/ReviewConsensusVariants.html
[fgbio-fastqtobam-link]: https://fulcrumgenomics.github.io/fgbio/tools/latest/FastqToBam.html
[fgbio-zipperbams-link]: https://fulcrumgenomics.github.io/fgbio/tools/latest/ZipperBams.html
[fgbio-demuxfastqs-link]: https://fulcrumgenomics.github.io/fgbio/tools/latest/DemuxFastqs.html
[fgbio-filterbam-link]: https://fulcrumgenomics.github.io/fgbio/tools/latest/FilterBam.html
[fgbio-clipbam-link]: https://fulcrumgenomics.github.io/fgbio/tools/latest/ClipBam.html
[fgbio-randomizebam-link]: https://fulcrumgenomics.github.io/fgbio/tools/latest/RandomizeBam.html
[fgbio-setmateinformation-link]: https://fulcrumgenomics.github.io/fgbio/tools/latest/SetMateInformation.html
[fgbio-updatereadgroups-link]: https://fulcrumgenomics.github.io/fgbio/tools/latest/UpdateReadGroups.html
[fgbio-collectalternatecontignames-link]: https://fulcrumgenomics.github.io/fgbio/tools/latest/CollectAlternateContigNames.html
[fgbio-updatefastacontignames-link]: https://fulcrumgenomics.github.io/fgbio/tools/latest/UpdateFastaContigNames.html
[fgbio-updatevcfcontignames-link]: https://fulcrumgenomics.github.io/fgbio/tools/latest/UpdateVcfContigNames.html
[fgbio-updategffcontignames-link]: https://fulcrumgenomics.github.io/fgbio/tools/latest/UpdateGffContigNames.html
[fgbio-updateintervallistcontignames-link]: https://fulcrumgenomics.github.io/fgbio/tools/latest/UpdateIntervalListContigNames.html
[fgbio-updatedelimitedfilecontignames-link]: https://fulcrumgenomics.github.io/fgbio/tools/latest/UpdateDelimitedFileContigNames.html
[fgbio-errorratebyreadposition-link]: https://fulcrumgenomics.github.io/fgbio/tools/latest/ErrorRateByReadPosition.html
[fgbio-estimatepoolingfractions-link]: https://fulcrumgenomics.github.io/fgbio/tools/latest/EstimatePoolingFractions.html
[fgbio-estimaternaseqinsertsize-link]: https://fulcrumgenomics.github.io/fgbio/tools/latest/EstimateRnaSeqInsertSize.html
[fgbio-pickilluminaindices-link]: https://fulcrumgenomics.github.io/fgbio/tools/latest/PickIlluminaIndices.html
[fgbio-picklongindices-link]: https://fulcrumgenomics.github.io/fgbio/tools/latest/PickLongIndices.html
[fgbio-findtechnicalreads-link]: https://fulcrumgenomics.github.io/fgbio/tools/latest/FastqToBam.html
[fgbio-sortbam-link]: https://fulcrumgenomics.github.io/fgbio/tools/latest/SortBam.html
[fgbio-makemixturevcf-link]: https://fulcrumgenomics.github.io/fgbio/tools/latest/MakeMixtureVcf.html
[fgbio-maketwosamplemixturevcf-link]: https://fulcrumgenomics.github.io/fgbio/tools/latest/MakeTwoSampleMixtureVcf.html
[fgbio-findswitchbackreads-link]: https://fulcrumgenomics.github.io/fgbio/tools/latest/FindSwitchbackReads.html

## Building
### Cloning the Repository
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