FinaleMe

KO | EN

gitlite — search

#javascript #ai #golang #android #deep-learning #linux #macos #java #windows #cli #awesome-list #openai #mcp #open-source

(★ 17)

No description available.

FinaleMe Latest Version Download

Download Latest Version (.zip)

// repository documentation

Was this content helpful?

★ 0 (0 ratings)

# FinaleMe

FinaleMe (FragmentatIoN AnaLysis of cEll-free DNA Methylation) predicts CpG methylation from cfDNA WGS fragment features using an HMM pipeline.

## Citation

Liu Y# et al. (2024) FinaleMe: Predicting DNA methylation by the fragmentation patterns of plasma cell-free DNA. Nature Communications. https://doi.org/10.1038/s41467-024-47196-6

## System requirements

- Java 21 or later (Oracle JDK 21 recommended): https://www.oracle.com/java/technologies/downloads/#java21
- Apache Maven 3.8+: 
https://maven.apache.org/install.html (or use the build .jar file from release)
- Optional for bigWig conversion speed/compatibility: `bedGraphToBigWig` (UCSC tools from here: https://hgdownload.soe.ucsc.edu/admin/exe/ and modify $PATH to allow the direct usage). If missing, FinaleMe falls back to built-in Java BigWig writing.
- Optional only for custom tissue reference-map generation: `wgbstools` (https://github.com/nloyfer/wgbs_tools) and `UXM_deconv` (https://github.com/nloyfer/UXM_deconv). They are not required for the default Steps 1-4 below.

## Quick install

```bash
git clone https://github.com/epifluidlab/FinaleMe.git
cd FinaleMe
./scripts/sync-vendored-repo.sh
mvn clean package
```

## Quick setup

Run one command to build FinaleMe and download required hg19/hg38 reference files into `data/`:

```bash
./scripts/setup_references.sh
```

## Test dataset

Download a chr22 BAM test file (a ~100X cfDNA WGS data from Snyder et al. 2016 Cell paper):

```bash
mkdir -p test results
curl -L "https://zenodo.org/records/6914806/files/BH01.chr22.bam?download=1" -o test/BH01.chr22.bam
curl -L "https://zenodo.org/records/6914806/files/BH01.chr22.bam.bai?download=1" -o test/BH01.chr22.bam.bai || samtools index test/BH01.chr22.bam
```

## Getting started

Set a jar variable once:

```bash
JAR="target/FinaleMe-0.61-jar-with-dependencies.jar"
```

### Step 1: Build CpG feature matrix

```bash
java -Xmx20G -cp "$JAR" \
  edu.northwestern.epifluidlab.finaleme.utils.CpgFeatureMatrixBuilder \
  data/hg19.2bit \
  data/CG_motif.hg19.common_chr.pos_only.bedgraph.gz \
  data/CG_motif.hg19.common_chr.pos_only.bedgraph.gz \
  test/BH01.chr22.bam \
  results/BH01.cpg_features.hg19.bed.gz \
  -stringentPaired \
  -excludeRegions data/wgEncodeDukeMapabilityRegionsExcludable_wgEncodeDacMapabilityConsensusExcludable.hg19.bed \
  -valueWigs methyPrior:0:data/wgbs_buffyCoat_jensen2015GB.methy.hg19.bw \
  -useNoChrPrefixBam \
  -wgsMode \
  -t 4
```

Output: `results/BH01.cpg_features.hg19.bed.gz`.

It will cost ~25 min for the test dataset.

### Step 2: Train HMM model

```bash
java -Xmx20G -cp "$JAR" \
  edu.northwestern.epifluidlab.finaleme.hmm.FinaleMe \
  results/BH01.FinaleMe.model \
  results/BH01.cpg_features.hg19.bed.gz \
  results/BH01.train.prediction.bed.gz \
  -miniDataPoints 7 -gmm -covOutlier 3 -t 4
```

Outputs: model `results/BH01.FinaleMe.model` and training prediction file.

It will cost < 1 min for the test dataset.

### Step 3: Decode CpG methylation

```bash
java -Xmx20G -cp "$JAR" \
  edu.northwestern.epifluidlab.finaleme.hmm.FinaleMe \
  results/BH01.FinaleMe.model \
  results/BH01.cpg_features.hg19.bed.gz \
  results/BH01.decode.prediction.bed.gz \
  -decodeModeOnly \
  -t 4 \
  -bwOutput \
  -chromSizeFile data/hg19.chrom.sizes \
```

Outputs:
- `results/BH01.decode.prediction.bed.gz`
- `results/BH01.decode.prediction.methy.bw`
- `results/BH01.decode.prediction.cov.bw`
- `results/BH01.decode.prediction.methy_count.bw`.

It will cost < 1 min for the test dataset.

### Step 4: Tissues-of-origin analysis

Using FinaleMe's beta-value deconvolution (`BetaValueDeconvolution`, recommended):

```bash
java -Xmx20G -cp "$JAR" \
  edu.northwestern.epifluidlab.finaleme.utils.BetaValueDeconvolution \
  -binarizeThreshold 0.1 \
  -markerRegions results/cgi_shore_atlas/Atlas.CGI_shore.U250.l3.hg19.tsv \
  -refBetas results/cgi_shore_atlas/reference_wgbs/betas/beta_list.txt \
  -refGroups results/cgi_shore_atlas/groups_fixed.csv \
  -cpgIndex data/CpG_index.hg19.bed.gz \
  -solver NNLS \
  -output results/BH01.deconv.beta.tsv \
  results/BH01.decode.prediction.bed.gz
```

Use [tutorial/tutorial_ref_maps.md](tutorial/tutorial_ref_maps.md) to generate the marker atlas (`-markerRegions`) and reference panel files (`-refBetas`, `-refGroups`).

## Full tutorial

For full option-by-option documentation, file format details, advanced workflows (including tabix fragment input files from FinaleDB), and troubleshooting, see:

- [tutorial/tutorial.md](tutorial/tutorial.md)

## License

For academic research, please refer to MIT license. For commercial usage, please contact the authors.

FinaleMe

FinaleMe Latest Version Download

Today's picks

Was this content helpful?

Recent Feedback

FinaleMe

FinaleMe Latest Version Download

Today's picks

Was this content helpful?

Recent Feedback

Download README