adam
ADAM is a genomics analysis platform with specialized file formats built using Apache Avro, Apache Spark, and Apache Parquet. Apache 2 licensed.
File Explorer
Download Latest Version (.zip)- ci.yml
- deploy.yml
- GenomicDatasetConverters.scala
- GenomicRDDConverters.scala
- JavaADAMContext.scala
- DataFrameConversionWrapper.scala
- JavaADAMCoverageConduit.java
- JavaADAMFeatureConduit.java
- JavaADAMFragmentConduit.java
- JavaADAMGenotypeConduit.java
- JavaADAMReadConduit.java
- JavaADAMSequenceConduit.java
- JavaADAMSliceConduit.java
- JavaADAMVariantConduit.java
- sorted.bam
- sorted.bam.bai
- JavaADAMContextSuite.scala
- pom.xml
- Assembly.scala
- pom.xml
- About.java
- ADAM2Fastq.scala
- ADAMMain.scala
- CountReadKmers.scala
- CountSliceKmers.scala
- Coverage.scala
- CramArgs.scala
- FileSystemUtils.scala
- FlagStat.scala
- MergeShards.scala
- PrintADAM.scala
- TransformAlignments.scala
- TransformFeatures.scala
- TransformFragments.scala
- TransformGenotypes.scala
- TransformSequences.scala
- TransformSlices.scala
- TransformVariants.scala
- View.scala
- artificial.counts.txt
- artificial.fa
- artificial.fa.fai
- bqsr1-r1.fq
- bqsr1-r2.fq
- bqsr1.sam
- chr5.phyloP46way.trunc.wigFix
- contigs.fa
- flag-values.sam
- gencode.v7.annotation.trunc10.bed
- log4j.properties
- small.vcf
- sorted.bam
- sorted.bam.bai
- sorted.counts.txt
- sorted.lex.vcf
- sorted.vcf
- AboutSuite.scala
- ADAM2FastqSuite.scala
- ADAMMainSuite.scala
- CountReadKmersSuite.scala
- CountSliceKmersSuite.scala
- CoverageSuite.scala
- MergeShardsSuite.scala
- ParquetLister.scala
- TransformAlignmentsSuite.scala
- TransformFeaturesSuite.scala
- TransformFragmentsSuite.scala
- TransformGenotypesSuite.scala
- TransformVariantsSuite.scala
- ViewSuite.scala
- .gitignore
- pom.xml
- DumpSchemasToProduct.scala
- DumpSchemasToProjectionEnums.scala
- Generator.scala
- ReflectSchema.scala
- pom.xml
- FastqInputFormat.java
- FastqRecordReader.java
- InterleavedFastqInputFormat.java
- ResettableCompressedSplitLineReader.java
- SingleFastqInputFormat.java
- Consensus.scala
- ConsensusGenerator.scala
- ConsensusGeneratorFromKnowns.scala
- ConsensusGeneratorFromReads.scala
- ConsensusGeneratorFromSmithWaterman.scala
- NormalizationUtils.scala
- UnionConsensusGenerator.scala
- SmithWaterman.scala
- SmithWatermanConstantGapScoring.scala
- SmithWatermanGapScoringFromFn.scala
- AlignmentConverter.scala
- DefaultHeaderLines.scala
- FastaConverters.scala
- FastqRecordConverter.scala
- FragmentConverter.scala
- TranscriptEffectConverter.scala
- VariantContextConverter.scala
- BEDInFormatter.scala
- BEDOutFormatter.scala
- CoverageDataset.scala
- FeatureDataset.scala
- FeatureParser.scala
- Features.scala
- GFF3HeaderWriter.scala
- GFF3InFormatter.scala
- GFF3OutFormatter.scala
- GTFInFormatter.scala
- GTFOutFormatter.scala
- NarrowPeakInFormatter.scala
- NarrowPeakOutFormatter.scala
- FragmentDataset.scala
- InterleavedFASTQInFormatter.scala
- Tab5InFormatter.scala
- Tab6InFormatter.scala
- IndelRealignmentTarget.scala
- ModPartitioner.scala
- RealignIndels.scala
- RealignmentTargetFinder.scala
- Aggregate.scala
- BaseQualityRecalibration.scala
- Covariate.scala
- CovariateKey.scala
- CovariateSpace.scala
- CycleCovariate.scala
- DinucCovariate.scala
- Observation.scala
- ObservationTable.scala
- RecalibrationTable.scala
- Recalibrator.scala
- ADAMBAMOutputFormat.scala
- ADAMCRAMOutputFormat.scala
- ADAMSAMOutputFormat.scala
- AlignmentDataset.scala
- AnySAMInFormatter.scala
- AnySAMOutFormatter.scala
- BAMInFormatter.scala
- BinQualities.scala
- FASTQInFormatter.scala
- FlagStat.scala
- MarkDuplicates.scala
- MDTagging.scala
- ReadDataset.scala
- ReferencePositionPair.scala
- RepairPartitions.scala
- SAMInFormatter.scala
- SingleReadBucket.scala
- FASTAInFormatter.scala
- FlankSlices.scala
- SequenceDataset.scala
- SliceDataset.scala
- ADAMVCFOutputFormat.scala
- GenotypeDataset.scala
- VariantContextDataset.scala
- VariantDataset.scala
- VCFInFormatter.scala
- VCFOutFormatter.scala
- ADAMContext.scala
- ADAMParquetInputFormat.scala
- ADAMSaveAnyArgs.scala
- GenomeBins.scala
- GenomicBroadcast.scala
- GenomicDataset.scala
- GenomicDatasetConversion.scala
- GenomicPartitioners.scala
- InFormatter.scala
- OutFormatter.scala
- ReferencePartitioner.scala
- RegionJoin.scala
- SAMHeaderWriter.scala
- ShuffleRegionJoin.scala
- TreeRegionJoin.scala
- VCFHeaderUtils.scala
- Alphabet.scala
- Attribute.scala
- Coverage.scala
- IndelTable.scala
- MdTag.scala
- NonoverlappingRegions.scala
- ReadGroupDictionary.scala
- ReferencePosition.scala
- ReferenceRegion.scala
- SAMFileHeaderWritable.scala
- SequenceDictionary.scala
- SnpTable.scala
- VariantContext.scala
- VCFHeaderWritable.scala
- FieldEnumeration.scala
- Projection.scala
- RichAlignment.scala
- RichCigar.scala
- RichVariant.scala
- ADAMKryoRegistrator.scala
- VariantContext.scala
- ADAMShell.scala
- ASCIITable.scala
- AttributeUtils.scala
- FileExtensions.scala
- FileMerger.scala
- GenomeFileReader.scala
- IndexedFastaFile.scala
- ManualRegionPartitioner.scala
- ParallelFileMerger.scala
- ParquetFileTraversable.scala
- ParquetLogger.scala
- PhredUtils.scala
- ReferenceFile.scala
- ReferenceMap.scala
- SequenceDictionaryReader.scala
- TextAlignment.scala
- TextRddWriter.scala
- TwoBitFile.scala
- small.bam
- gvcf_multiallelic.g.vcf
- gvcf_multiallelic_noPLs.g.vcf
- multiallelic.vcf
- sorted.2.bai
- sorted.2.bam
- sorted.bam
- sorted.bam.bai
- small.INFO_flag.vcf
- truth_small_variants.vcf
- 1.vcf
- 2.vcf
- 3.vcf
- zero.vcf
- artificial.cram
- artificial.fa
- artificial.fa.fai
- artificial.README.txt
- artificial.realigned.sam
- artificial.sam
- badheader.sam
- bqsr1-r1.fq
- bqsr1-r2.fq
- bqsr1-ref.observed
- bqsr1.sam
- bqsr1.snps
- bqsr1.vcf
- bqsr1.vcf.tbi
- chr20.250k.fa.gz
- chromInfo.txt
- combined_2018-05-18.9900-10050.fastq
- ctg123.fasta.gff3
- dict_with_accession.dict
- dvl1.200.bed
- dvl1.200.gff3
- dvl1.200.gtf
- env_test_command.sh
- example_intervals.list
- fastq_nobases.fq
- fastq_noqual.fq
- fastq_sample1.fq
- fastq_sample1.fq.bgz
- fastq_sample1.fq.bz2
- fastq_sample1.fq.gz
- fastq_sample2.fq
- fastq_sample3.fq
- fastq_sample4.fq
- fastq_to_usam.py
- gencode.chr20.transcript_names.head10.txt
- gencode.v19.annotation.chr20.250k.gtf
- gencode.v19.pc_transcripts.250k.fa.gz
- gencode.v7.annotation.trunc10.bed
- HG001_GRCh38_GIAB_highconf_CG-IllFB-IllGATKHC-Ion-10X-SOLID_CHROM1-X_v.3.3.2_all.fixed-phase-set.excerpt.vcf
- HG001_GRCh38_GIAB_highconf_CG-IllFB-IllGATKHC-Ion-10X-SOLID_CHROM1-X_v.3.3.2_all.fixed-phase-set.excerpt.vcf.README
- hg19.chrM.2bit
- hg19.genome
- hg19.genome.txt
- HLA_DQB1_05_01_01_02.dict
- HLA_DQB1_05_01_01_02.fa
- HLA_DQB1_05_01_01_02.fa.fai
- Homo_sapiens.GRCh37.75.trun100.gtf
- Homo_sapiens.GRCh37.75.trun20.gtf
- hs37d5.dict
- hs38DH_chr1_10.fa
- Hs_Ensembl_example_genes.gtf
- human_g1k_v37_chr1_59kb.2bit
- human_g1k_v37_chr1_59kb.fasta
- improper_pairs_1.fq
- improper_pairs_2.fq
- inf_float_values.vcf
- interleaved_fastq_sample1.ifq
- interleaved_fastq_sample1.ifq.bgz
- interleaved_fastq_sample1.ifq.bz2
- interleaved_fastq_sample1.ifq.gz
- interleaved_fastq_sample1.ifq.output
- interleaved_fastq_sample2.ifq
- interleaved_fastq_sample2.ifq.output
- interleaved_fastq_sample3.ifq
- interleaved_fastq_sample3.ifq.output
- interleaved_fastq_sample4.ifq
- interleaved_fastq_sample4.ifq.output
- interleaved_fastq_sample5.ifq
- interleaved_fastq_sample5.ifq.output
- legacy.fa
- log4j.properties
- multi_chr.sam
- multiline_fastq.fq
- NA12878.1_854950_855150.sam
- NA12878.1_922305.G_GC_hom.sam
- NA12878.chr22.tiny.freebayes.vcf
- NA12878.sam
- nan_float_values.vcf
- ordered.sam
- proper_pairs_1.fq
- proper_pairs_2.fq
- queryname.sam
- random.vcf
- read_names_with_index_sequences_interleaved.fq
- read_names_with_index_sequences_pair1.fq
- read_names_with_index_sequences_pair2.fq
- readname_sorted.sam
- reads-0-2-0
- reads12.sam
- reads12_diff1.sam
- reads13.sam
- reads21.sam
- sample1.query.sam
- sample1.queryname.sam
- sample_coverage.bed
- SeqCap_EZ_Exome_v3.hg19.interval_list
- single_fastq_sample1.fq.output
- single_fastq_sample2.fq.output
- single_fastq_sample3.fq.output
- single_fastq_sample4.fq.output
- small.1.bed
- small.1.narrowPeak
- small.1.sam
- small.1_12.bed
- small.addctg.vcf
- small.badheader.sam
- small.sam
- small.vcf
- small_missing.vcf
- small_realignment_targets.intervals
- small_realignment_targets.pileup
- small_realignment_targets.sam
- small_realignment_targets_README.txt
- small_snpeff.vcf
- sorted-variants.lex.vcf
- sorted-variants.vcf
- sorted.lex.vcf
- sorted.sam
- sorted.vcf
- tab5_to_usam.py
- tab6_to_usam.py
- tag.sam
- tags.sam
- test.compressed.bcf
- test.conf
- test.uncompressed.bcf
- test.vcf
- test.vcf.bgz
- test.vcf.bgzf.gz
- test.vcf.gz
- test_command.sh
- test_rowgroup_rangeindex.1.txt
- timeout.py
- trinity.fa
- unmapped.sam
- unordered.sam
- unsorted.sam
- wgEncodeOpenChromDnaseGm19238Pk.trunc10.narrowPeak
- wgs_calling_regions.hg38.interval_list
- ConsensusGeneratorFromKnownsSuite.scala
- ConsensusGeneratorFromReadsSuite.scala
- ConsensusSuite.scala
- NormalizationUtilsSuite.scala
- SmithWatermanSuite.scala
- AlignmentConverterSuite.scala
- FastqRecordConverterSuite.scala
- FragmentConverterSuite.scala
- TranscriptEffectConverterSuite.scala
- VariantContextConverterSuite.scala
- CoverageDatasetSuite.scala
- FeatureDatasetSuite.scala
- GFF3HeaderWriterSuite.scala
- FragmentDatasetSuite.scala
- IndelRealignmentTargetSuite.scala
- ModPartitionerSuite.scala
- RealignIndelsSuite.scala
- BaseQualityRecalibrationSuite.scala
- CycleCovariateSuite.scala
- DinucCovariateSuite.scala
- RecalibrationTableSuite.scala
- RecalibratorSuite.scala
- AlignmentDatasetSuite.scala
- BinQualitiesSuite.scala
- FlagStatSuite.scala
- MarkDuplicatesSuite.scala
- MDTaggingSuite.scala
- ReadDatasetSuite.scala
- RepairPartitionsSuite.scala
- SingleReadBucketSuite.scala
- FlankSlicesSuite.scala
- SequenceDatasetSuite.scala
- SliceDatasetSuite.scala
- GenotypeDatasetSuite.scala
- VariantContextDatasetSuite.scala
- VariantDatasetSuite.scala
- ADAMContextSuite.scala
- GenomicDatasetSuite.scala
- GenomicPositionPartitionerSuite.scala
- InnerShuffleRegionJoinSuite.scala
- InnerTreeRegionJoinSuite.scala
- LeftOuterShuffleRegionJoinAndGroupByLeftSuite.scala
- LeftOuterShuffleRegionJoinSuite.scala
- OuterRegionJoinSuite.scala
- RightOuterTreeRegionJoinSuite.scala
- SortedGenomicDatasetSuite.scala
- TreeRegionJoinSuite.scala
- InterleavedFastqInputFormatSuite.scala
- SingleFastqInputFormatSuite.scala
- AlphabetSuite.scala
- CoverageSuite.scala
- IndelTableSuite.scala
- MdTagSuite.scala
- NonoverlappingRegionsSuite.scala
- ReadGroupDictionarySuite.scala
- ReferencePositionSuite.scala
- ReferenceRegionSuite.scala
- SequenceDictionarySuite.scala
- SnpTableSuite.scala
- RichAlignmentSuite.scala
- RichCigarSuite.scala
- ADAMFunSuite.scala
- AttributeUtilsSuite.scala
- FileExtensionsSuite.scala
- FileMergerSuite.scala
- IndexedFastaFileSuite.scala
- ParallelFileMergerSuite.scala
- PhredUtilsSuite.scala
- TwoBitFileSuite.scala
- .gitignore
- pom.xml
- assembly.xml
- pom.xml
- __init__.py
- adamContext_test.py
- alignmentDataset_test.py
- coverageDataset_test.py
- featureDataset_test.py
- genotypeDataset_test.py
- variantDataset_test.py
- .gitignore
- __init__.py
- adamContext.py
- ds.py
- find_adam_home.py
- models.py
- stringency.py
- __init__.py
- .gitignore
- Makefile
- MANIFEST.in
- pom.xml
- README.md
- setup.py
- version.py
- adam-context.R
- ds.R
- generics.R
- helpers.R
- test_adamContext.R
- test_alignmentDataset.R
- test_featureDataset.R
- test_genotypeDataset.R
- test_variantDataset.R
- testthat.R
- DESCRIPTION
- NAMESPACE
- .gitignore
- pom.xml
- adam-shell
- adam-submit
- adamR
- find-adam-assembly.sh
- find-adam-egg.sh
- find-adam-home
- find-spark.sh
- pyadam
- favicon.ico
- logo.png
- bqsr.rst
- dm.rst
- joins.rst
- reads.rst
- ri.rst
- join_examples.png
- join_rdds.png
- adamContext.rst
- genomicDataset.rst
- joins.rst
- overview.rst
- pipes.rst
- python.rst
- grdd.pdf
- grdd.png
- stack-model.pdf
- stack-model.png
- evidence.rst
- overview.rst
- schemas.rst
- stackModel.rst
- bam.pdf
- bam.png
- bed.pdf
- bed.png
- gff.pdf
- gff.png
- plot-speedup.py
- speedup-bqsr.pdf
- speedup-bqsr.png
- speedup-ir.pdf
- speedup-ir.png
- speedup-md.pdf
- speedup-md.png
- vcf.pdf
- vcf.png
- algorithms.rst
- storage.rst
- actions.rst
- conversions.rst
- overview.rst
- printers.rst
- aws.rst
- gcp.rst
- slurm.rst
- toil.rst
- yarn.rst
- cli.rst
- library.rst
- overview.rst
- file_benchmarks.py
- bdgenomics-stack.key
- bdgenomics-stack.png
- stack-model.ai
- example.rst
- pip.rst
- source.rst
- bibliography.bib
- .gitignore
- citing.rst
- conf.py
- index.rst
- Makefile
- references.rst
- requirements.txt
- template.tex
- fastq-interleaver.py
- make-flag-values-sam.py
- move_to_scala_2.11.sh
- move_to_scala_2.12.sh
- move_to_spark_2.sh
- move_to_spark_3.sh
- release.sh
- .gitignore
- CHANGES.md
- CODE_OF_CONDUCT.md
- CONTRIBUTING.md
- KEYS
- LICENSE.txt
- LICENSE_header.txt
- pom.xml
- README.md
- SUPPORT.md
π Installation Guide
1. Get the code
git clone https://github.com/bigdatagenomics/adam
Downloads the entire project code from GitHub to your computer.
cd adam
Moves into the project folder you just downloaded.
2. Maven (Java)
Medium RecommendedPrerequisites
- Git Needed to download the project code from GitHub.
- JDK (Java) Required to build and run Java projects.
- Maven The build tool used for the mvn command.
$ mvn install
Installs dependencies and builds the project using Maven.
A BUILD SUCCESS message means it worked. The output is created under target/.
Pulled directly from this repo's README.
3. Python
EasyPrerequisites
pip install -r docs/requirements.txt
Installs the Python libraries listed in requirements.txt (or similar).
python <μ€νν νμΌλͺ
>.py # READMEμμ μ νν μ€ν νμΌλͺ
μ νμΈνμΈμ
Runs the Python script (or module).
If it runs without errors and prints output in the terminal, it worked.
4. Make
MediumPrerequisites
- Git Needed to download the project code from GitHub.
- Make Usually pre-installed on Linux/macOS. On Windows, install separately (e.g. via MSYS2 or WSL).
cd adam-python
This project's files live in a subfolder, so move into it first.
make
Compiles the code based on the generated build configuration to produce an executable.
If it finishes without errors, it worked. Try running the generated executable directly.
// repository documentation
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