Description

Computational framework for tracking and quantifying DNA damage patterns among ancient DNA sequencing reads generated by Next-Generation Sequencing platforms.

Input

name:type
description
pattern

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false]

bam{:bash}

:file

BAM file

*.{bam}

fasta{:bash}

:file

Fasta file, the reference the input BAM was mapped against

*.{fasta}

Output

name:type
description
pattern

runtime_log{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false]

results_*/Runtime_log.txt{:bash}

:file

Log file with a summary of command lines used and timestamps.

Runtime_log.txt

fragmisincorporation_plot{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false]

results_*/Fragmisincorporation_plot.pdf{:bash}

:file

A pdf file that displays both fragmentation and misincorporation patterns.

Fragmisincorporation_plot.pdf

length_plot{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false]

results_*/Length_plot.pdf{:bash}

:file

A pdf file that displays length distribution of singleton reads per strand and cumulative frequencies of C->T at 5’-end and G->A at 3’-end are also displayed per strand.

Length_plot.pdf

misincorporation{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false]

results_*/misincorporation.txt{:bash}

:file

Contains a table with occurrences for each type of mutations and relative positions from the reads ends.

misincorporation.txt

lgdistribution{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false]

results_*/lgdistribution.txt{:bash}

:file

Contains a table with read length distributions per strand.

lgdistribution.txt

dnacomp{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false]

results_*/dnacomp.txt{:bash}

:file

Contains a table of the reference genome base composition per position, inside reads and adjacent regions.

dnacomp.txt

stats_out_mcmc_hist{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false]

results_*/Stats_out_MCMC_hist.pdf{:bash}

:file

A MCMC histogram for the damage parameters and log likelihood.

Stats_out_MCMC_hist.pdf

stats_out_mcmc_iter{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false]

results_*/Stats_out_MCMC_iter.csv{:bash}

:file

Values for the damage parameters and log likelihood in each MCMC iteration.

Stats_out_MCMC_iter.csv

stats_out_mcmc_trace{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false]

results_*/Stats_out_MCMC_trace.pdf{:bash}

:file

A MCMC trace plot for the damage parameters and log likelihood.

Stats_out_MCMC_trace.pdf

stats_out_mcmc_iter_summ_stat{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false]

results_*/Stats_out_MCMC_iter_summ_stat.csv{:bash}

:file

Summary statistics for the damage parameters estimated posterior distributions.

Stats_out_MCMC_iter_summ_stat.csv

stats_out_mcmc_post_pred{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false]

results_*/Stats_out_MCMC_post_pred.pdf{:bash}

:file

Empirical misincorporation frequency and posterior predictive intervals from the fitted model.

Stats_out_MCMC_post_pred.pdf

stats_out_mcmc_correct_prob{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false]

results_*/Stats_out_MCMC_correct_prob.csv{:bash}

:file

Position specific probability of a C->T and G->A misincorporation is due to damage.

Stats_out_MCMC_correct_prob.csv

dnacomp_genome{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false]

results_*/dnacomp_genome.csv{:bash}

:file

Contains the global reference genome base composition (computed by seqtk).

dnacomp_genome.csv

rescaled{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false]

results_*/*rescaled.bam{:bash}

:file

Rescaled BAM file, where likely post-mortem damaged bases have downscaled quality scores.

*.{bam}

pctot_freq{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false]

results_*/5pCtoT_freq.txt{:bash}

:file

Contains frequencies of Cytosine to Thymine mutations per position from the 5’-ends.

5pCtoT_freq.txt

pgtoa_freq{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false]

results_*/3pGtoA_freq.txt{:bash}

:file

Contains frequencies of Guanine to Adenine mutations per position from the 3’-ends.

3pGtoA_freq.txt

fasta{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false]

results_*/*.fasta{:bash}

:file

Alignments in a FASTA file, only if flagged by -d.

*.{fasta}

folder{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false]

*/{:bash}

:directory

Folder created when —plot-only, —rescale and —stats-only flags are passed.

*/

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

Tools

maintainer
Github user darcy220606
get in touch
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