Software for analysis of cell-free DNA (cfDNA)

Below is the repository of software tools for analysis of sequenced cell-free DNA (cfDNA). This collection is part of NucPosDB, a manually curated database of experimental nucleosome maps in vivo, cfDNA and computational tools related to nucleosome positioning

Jump to: NucPosDB front page | stable nucleosomes of the human genome | experimental nucleosome maps in vivo | experimental cfDNA datasets | tools for analysis of nucleosome mapping experiments | tools for prediction of nucleosome maps from DNA sequence | tools for analysis of sequenced cfDNA

**How to cite: Shtumpf M., Piroeva K.V., Agrawal S.P., Jacob D.R., Teif V.B. (2022). NucPosDB: a database of nucleosome positioning in vivo and nucleosomics of cell-free DNA. Chromosoma 13119-28 | open access article


NameKey featuresProgramming languageAnalysis typeCitation
BIC-seq2Normalization oh high-throughput sequencing (HTS) data and detect CNVs with or without a control gene. Avoids high variability of reads in the bins.ShellCopy number variationsXi et al., 2016
CancerDetectorImproves ctDNA fraction estimation and identifies outliner markers.RMethylationLi et al., 2018
CancerLocatorSimultaneously infers the proportion and tissue of origin of ctDNA.JavaMethylationKang et al., 2017
CELFIEEstimates cell type proportion from both whole genome cfDNA input and reference data. Do not rely on CpG site curation, estimates unknown cell types that are not available in reference. Estimate known and unknown cell type in low coverage and noisy data.PythonDNA methylationCaggiano et al., 2020
cfCHIP-seqChIP–seq offers superior data quality to chromatin immunoprecipitation and eliminate bias in fragmentation and sequencing.RDNA-binding proteins and histone modificationsSadeh et al., 2021
cfDNA-FEPcfDNA fragment end profiling in genomic regions of interestRcfDNA fragmentation profilesZhitnyuk et al., 2022
cfDNApipeAccompanied with a GC-bias
correction approach, distinguishes differential methylation regions between subject and control samples
PythonCopy number variations, DNA methylation, Nucleosome positioning
Ahang et al., 2021
CNAcliniccarry out an analysis of CNA providing functionality tailored for shallow whole genome sequencing as well as the capacity for multi-faceted visualization and data interrogation.RDNA fragmentation and CNVsMouliere et al., 2018
CNVkitTargeted re-sequencing, which leaves gaps in coverage between the regions chosen for enrichment and introduces biases. Uses both the targeted reads and the non-specifically captured off-target reads to infer copy number.PythonCopy number variationsTalevich et al., 2016
DeepSNVDetection of subclonal single nucleotide variants in heterogenous cell populations.PythonSomatic mutationGerstung et al., 2012
DELFIDetection of the abnormalities of cfDNA fragmentation profiles at genome-wide levelRNucleosome positioningCristiano et al., 2019
GriffinA flexible framework for nucleosome profiling of cell-free DNAPythonNucleosome positioningDoebley et al., 2021
ichorCNAEstimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing.R, ShellTumor fractionAdalsteinsson et al., 2017
INVARCombines locus-based noise filtering, strand selection, and enrichment of mutant fragments using biological characteristics of ctDNA. The detection limit in each sample can be estimated independently based on the number of informative reads sequenced across multiple patient-specific loci.Python, RSomatic mutationWan et al., 2020
JointSN-VMixGermline and somatic events can be identified and distinguished.Python, CSomatic mutationRoth et al., 2012
MAGERIAn efficient pipeline for analysis of unique molecular identifier or UMI-encoded data by filling the gaps.JavaUltra-rare somatic mutationShugay et al., 2017
MRDetectAllows genome-wide mutational integration, enabling ultra-sensitive detectionSomatic mutationZviran et al., 2020
MSIsensor-ctDetection of microsatellite instability (MSI) status in cfDNA sequencing data with MSIscore threshold of 20%.C++Microsatellite Instability (MSI)Han et al., 2021
Mutation-SeqFeature-based classification. Integrate different features like base qualities, mapping qualities, strand bias, and tailed distance features.Python, C++, CSomatic mutationDing et al., 2012
MutTectHigh sensitivityJavaSomatic mutationCibulskis et al., 2013
NDRquantQuantification of the content of circulating tumor DNA (ctDNA) based on tissue-specific cfDNA degradation of nucleosome depleted regions (NDR).ShellNucleosome PositioningZhu et al., 2021
NucToolsAnalysis of chromatin feature occupancy profiles from high-throughput sequencing dataPerl, Shell, R ,CSSNucleosome positioningVainshtein et al., 2017
PlasmaSeqEstimates tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencingR, HTML, C, Perl, TeX, CSS, OtherTumor fractionMoser et al., 2017
Python ScriptsAnalysis of epigenetic signals captured by fragmentation patterns of cfDNA and develop in vivo nucleosome footprint that informs TOO.PythonNucleosome positioningSnyder et al., 2016
QDNA-seqWhole-genome sequencing (WGS) faces lack of completion and errors in human reference genome and has biases in the sequencing procedure. Simultaneously corrects Sequence mappability and GC content biases.RCopy number variationsScheinin et al., 2014
SeuratDetection of cancer related different somatic events of point mutations such as base substitution, insertion and deletion. Detection of loss of heterogenicity events, translocations and large deletions.RSomatic mutationChristoforides et al., 2013
ShimmerPrediction of SNVs with high sensitivity and accuracy in highly contaminated or heterogenous samples.Python, R, CSomatic mutationHansen et al., 2013
SomaticSniperCompares and identifies the unique (mutation) sites in tumour and normal pairs of samples.  Python, CSingle nucleotide variantsLarson et al., 2012
SpikyConverts read counts to picomoles of DNA fragments, while adjusting for fragment properties that affect enrichment.R, MakefileSpike-in DNA controlsWilson et al., 2021
StrelkaEnable detection of longer somatic indels and open break ends in contigs obtained from the routine de-novo assembly.Python, C++Somatic mutation and copy number variationsSaunders et al., 2012
TranscriptionFactorProfilingProfiling of transcription factor binding sites in cell-free DNAPython, R, ShellTranscription factor profilingUlz et al., 2019
UMI-toolsLow ctDNA content and sequencing artefacts limit analytical sensitivity. To overcome this, unique molecular identifiers (UMIs) are added into the adapters to tag individual cfDNA. UMI-tools identifies sequencing errors in the UMI sequences by comparing the sequences of PCR duplicates with UMI sequences to improve quantification accuracy.PythonSomatic mutationSmith et al., 2017
VarScan2Detection of somatic mutations and copy number alterations in tumour and normal pairs of samples.Python, RSingle nucleotide variantsKoboldt et al., 2012
WisecondorXOptimization of segmentation by reducing noise from problematic bins and lowering computing time.Python, RCopy number variationsRaman et al., 2019
LIQUORICEDetection of epigenetic signatures in liquid biopsies based on whole-genome sequencing dataPython, ShellEpigenetic signaturesPeneder, Bock and Tomazou, 2022
iWhaleComputational pipeline for detection and annotation of somatic variants in cancer WES dataPython, DockerfileSomatic mutationBinatti et al., 2021
MSK-GRAIL-TECHVALHigh-intensity sequencing reveals the sources of plasma circulating cell-free DNA variantsRCopy number variationsRazavi et al., 2019