Nextflow Modules
Showing module(s) with keyword "ancient DNA"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| nf-core/amps | Process | malt MaltExtract HOPS amps alignment metagenomics ancient DNA aDNA palaeogenomics archaeogenomics microbiome authentication damage edit distance post Post-processing visualisation | Post-processing script of the MaltExtract component of the HOPS package |
| nf-core/atlas/pmd | Process | ancient DNA post mortem damage bam | Estimate the post-mortem damage patterns of DNA |
| nf-core/damageprofiler | Process | damage deamination miscoding lesions C to T ancient DNA aDNA palaeogenomics archaeogenomics palaeogenetics archaeogenetics | A Java based tool to determine damage patterns on ancient DNA as a replacement for mapDamage |
| nf-core/dedup | Process | dedup deduplication pcr duplicates ancient DNA paired-end bam | DeDup is a tool for read deduplication in paired-end read merging (e.g. for ancient DNA experiments). |
| nf-core/endorspy | Process | endogenous DNA ancient DNA percent on target statistics | endorS.py calculates endogenous DNA from samtools flagstat files and print to screen |
| nf-core/leehom | Process | ancient DNA adapter removal clipping trimming merging collapsing preprocessing bayesian | Bayesian reconstruction of ancient DNA fragments |
| nf-core/malt/build | Process | malt alignment metagenomics ancient DNA aDNA palaeogenomics archaeogenomics microbiome database | MALT, an acronym for MEGAN alignment tool, is a sequence alignment and analysis tool designed for processing high-throughput sequencing data, especially in the context of metagenomics. |
| nf-core/maltextract | Process | malt MaltExtract HOPS alignment metagenomics ancient DNA aDNA palaeogenomics archaeogenomics microbiome authentication damage edit distance | Tool for evaluation of MALT results for true positives of ancient metagenomic taxonomic screening |
| nf-core/malt/run | Process | malt alignment metagenomics ancient DNA aDNA palaeogenomics archaeogenomics microbiome | MALT, an acronym for MEGAN alignment tool, is a sequence alignment and analysis tool designed for processing high-throughput sequencing data, especially in the context of metagenomics. |
| nf-core/mapdamage2 | Process | ancient DNA DNA damage NGS damage patterns bam | Computational framework for tracking and quantifying DNA damage patterns among ancient DNA sequencing reads generated by Next-Generation Sequencing platforms. |
| nf-core/multivcfanalyzer | Process | vcf ancient DNA aDNA SNP GATK UnifiedGenotyper SNP table | SNP table generator from GATK UnifiedGenotyper with functionality geared for aDNA |
| nf-core/pydamage/analyze | Process | ancient DNA aDNA de novo assembly filtering damage deamination miscoding lesions C to T palaeogenomics archaeogenomics palaeogenetics archaeogenetics | Damage parameter estimation for ancient DNA |
| nf-core/pydamage/filter | Process | ancient DNA aDNA de novo assembly filtering damage deamination miscoding lesions C to T palaeogenomics archaeogenomics palaeogenetics archaeogenetics | Damage parameter estimation for ancient DNA |
| nf-core/topas/gencons | Process | consensus fasta ancient DNA | Create fasta consensus with TOPAS toolkit with options to penalize substitutions for typical DNA damage present in ancient DNA |