GATK is a software toolkit used to perform variant calling and genotyping.ANGSD (Analysis of Next Generation Sequencing Data) is a multipurpose genetic data analysis tool that can be used for genotyping.
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.PyDamage software to automate the process of contig damage identification and estimation.DamageProfiler used to calculate damage profiles of mapped ancient DNA reads.mapDamage2 tracks and quantifies DNA damage patterns.metaSpades assembles DNA sequences from mixed sources into contigs.MEGAHIT assembles DNA sequences from mixed sources into contigs (contiguous stretches of DNA) compatibile with ancient DNA.Bowtie2 aligns DNA sequences to a reference sequence.BWA aln and samse/sampe are commonly chosen algorithms for ancient DNA analysis BWA (Burrows-Wheeler Aligner) aligns DNA sequences 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.paleoMIX is a pipeline for quality filtering and mapping ancient DNA data to a reference sequence.nf-core/eager (Efficient Ancient GenomE Reconstruction) is a GUI wrapper software for quality filtering and mapping sequence data to a reference sequence.Initial data handling and quality assessment CLC Genomics Workbench is a commercially available software suite for analyzing genomic data.Geneious is a commercially available software suite for analyzing genomic data.If you have add additional resources to suggest, please send your suggestions to Ancient DNA Below are a collection of commonly used software resources, including with links for their download. Many tools, programs, pipelines, and software suites are used in the analysis of ancient biomolecules.
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