Data analysis tools and pipelines
Many tools, programs, pipelines, and software suites are used in the analysis of ancient biomolecules. Below are a collection of commonly used software resources, including with links for their download. If you have add additional resources to suggest, please send your suggestions to webmaster@isbarch.org.
Ancient DNA
Multipurpose GUI platforms
- Geneious is a commercially available software suite for analyzing genomic data
- CLC Genomics Workbench is a commercially available software suite for analyzing genomic data
Initial data handling and quality assessment
- nf-core/eager (Efficient Ancient GenomE Reconstruction) is a GUI wrapper software for quality filtering and mapping sequence data to a reference sequence
- paleoMIX is a pipeline for quality filtering and mapping ancient DNA data to a reference sequence
- PreSeq is a tool that estimates DNA library complexity, essentially allowing users to model the costs and genome recovery potential of a given archaeological sample
DNA sequence alignment
- BWA (Burrows-Wheeler Aligner) aligns DNA sequences to a reference sequence. BWA aln and samse/sampe are commonly chosen algorithms for ancient DNA analysis
- Bowtie2 aligns DNA sequences to a reference sequence
DNA sequence assembly
- MEGAHIT assembles DNA sequences from mixed sources into contigs (contiguous stretches of DNA); compatibile with ancient DNA
- metaSpades assembles DNA sequences from mixed sources into contigs
Ancient DNA damage
- mapDamage2 tracks and quantifies DNA damage patterns
- DamageProfiler used to calculate damage profiles of mapped ancient DNA reads
- PyDamage software to automate the process of contig damage identification and estimation
- PMD Tools computes ancient DNA damage patterns, and implements a likelihood framework incorporating postmortem damage (PMD), base quality scores and biological polymorphism to identify degraded DNA sequences that are unlikely to originate from modern contamination
Variant calling and genotyping
- ANGSD (Analysis of Next Generation Sequencing Data) is a multipurpose genetic data analysis tool that can be used for genotyping.
- GATK is a software toolkit used to perform variant calling and genotyping. It can be used to estimate genotype likelihoods for phenotype-associated SNPs from ancient individuals
- pileupCaller is a tool used to sample alleles from low coverage data
Sex, kinship, and contamination
- ry_compute is a tool that estimates genetic sex from high-throughput DNA sequence data
- lcMLkin (Maximum Likelihood Estimation of Relatedness) uses genotype likelihoods to infer genetic relatedness from low coverage sequencing data
- READ (Relationship Estimation from Ancient DNA) estimates genetic kinship between a pair of individuals represented by low coverage sequencing data
- ANGSD (Analysis of Next Generation Sequencing Data) is a multipurpose genetic data analysis tool; its contamination module can be used to estimate nuclear contamination in males
- Schmutzi performs mitochondrial consensus calling and estimates mitochondrial contamination for ancient DNA
- SourceTracker2 estimates source contributions to a metagenomic sample and can be used to identify environmental contaminants in mixed microbial communities, such as dental calculus and paleofeces
- SourcePredict classifies and predicts the origin of metagenomic samples given a reference dataset of known origins using machine learning classification on dimensionally reduced datasets
- Decontam identifes contaminant sequences in a sample based on sequences identified in blanks and controls
- AuthentiCT: Provides an estimate of proportion of present-day DNA contamination in ancient DNA datasets using deamination patterns.
- KIN: Estimates genetic relatedness from ancient DNA data along with locations of IBD sharing and long runs of homozygosity
Ancestry and admixture
- ADMIXTURE estimates individual ancestries from SNP datasets
- Haplogrep2 classifies mitochondrial haplogroups using SNP datasets
- Haplofind assigns mitochondrial haplogroups using DNA sequence data
- yHaplo estimates the Y-haplogroup of males from SNP datasets
- smartPCA is a program within the EIGENSOFT software package that can be used to perform principal components analysis (PCA) on genetic data from ancient populations
- AdmixTools is a toolkit for infering admixture. It is used to calculate f3-, f4-, and D-statistics, and it includes the programs qpGraph, qpAdm, qp3pop, and qp3Dstat-
- TreeMix is used to infer patterns of population splits and mixtures in the history of a set of populations
Epigenetics
- epiPaleomix is a pipeline for generating nucleosome and methylation maps from ancient genomic data
Population and evolutionary history
- BEAST2 is a Bayesian phylogenetic analysis software package used to date population divergence between samples of known ages, and it is also used to model changes in effective population sizes through time
- MEGA is a multi-function software suite for analyzing sequence data, including phylogenetic tree-building
- RevBayes is a modeling, simulation and Bayesian inference software for phylogenetic analysis
- SimCoal2 is a coalescent modeling program for simulating recombination patterns under different demographic models, including migration events
- Bayesian Serial SimCoal (BayeSSC) is a modification of SimCoal that allows flexible coalescent modelling from different priors; it can incorporate ancient datasets to estimate the timing and magnitude of past demographic events
- PSMC (Pairwise Sequentially Markovian Coalescent) infers population size history from a diploid genome
- MSMC (Multiple Sequentially Markovian Coalescent) infers population size history and gene flow from multiple genomes
- RAxML (Randomized Axelerated Maximum Likelihood) infers phylogeny for large datasets using maximum likelihood
- GenErode a bioinformatics pipeline for investigating genome erosion in endangered and extinct species
Species identification and metagenomics
- BLAST (Basic Local Alignment Tool) identifies regions of similarity between a query sequence and reference database
- DIAMOND is an ultrafast DNA aligner that aligns translated DNA sequences to a protein sequence database
- MALT (MEGAN ALignment Tool) rapidly aligns DNA sequences to a reference database. It is especially useful for large metagenomic datasets
- MEGAN is a multi-function software suite for analyzing metagenomic data
- sam2lca is a program performing reference sequence disambiguation for reads mapping to multiple reference sequences in a shotgun metagenomics sequencing dataset; it takes as input the common SAM sequence alignment format and applies the lowest common ancestor algorithm
- metaPhlAn3 uses marker genes from reference genomes to profile microbial communities in metagenomic data
- Kraken2 is a taxonomic sequence classifier that assigns taxonomic labels to short DNA reads by examining the k-mers within a read and querying a database with those k-mers
- KrakenUniq is a metagenomics classifier that combines the fast k-mer-based classification of Kraken with an efficient algorithm for assessing the coverage of unique k-mers found in each species in a dataset
- SPARSE is a tool for identifying pathogen sequences in ancient metagenomics data sets
- metaBIT is a taxonomic profiling and visualization software for metagenomics data sets
Visualization tools
- IGV (Integrative Genomics Viewer) is a high-performance interactive tool for the visual exploration of genomic data
- Krona is a visualization tool that allows hierarchical data to be explored through interactive, mulit-layered pie charts.It is especially useful for visualizing taxonomically assigned metagenomics data
- GrapeTree is an interactive tree visualization program that supports manipulation of tree layout and metadata
Ancient Proteins
- MASCOT is a search engine for the identification, characterisation and quantitation of proteins using mass spectrometry data
- Max Quant is a quantitative proteomics software package designed for analyzing large mass-spectrometric data sets
- PEAKS is a proteomics software program for tandem mass spectrometry designed for peptide sequencing, protein identification and quantification
- Byonic is a MS/MS search engine
- mMass is open-source software primarily used for analyzing MALDI-TOF data in ZooMS analysis