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nf-core/mapdamage2 @ 0.0.0-6c4ed3a

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

ancient DNA DNA damage NGS damage patterns bam
Latest version: 0.0.0-6c4ed3a
Total downloads: 9
Source: nf-core/modules
Authors: @darcy220606
Maintainers: @darcy220606

Summary

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

Get started

Add the following snippet to your workflow script to include this module.

include { MAPDAMAGE2 } from 'nf-core/mapdamage2'

License

MIT License

Process
Name MAPDAMAGE2
Input 2 channels
#1 tuple
meta map

Groovy Map containing sample information e.g. [ id:'test', single_end:false]
bam file

BAM file

 *.{bam}
fasta file

Fasta file, the reference the input BAM was mapped against

 *.{fasta}
Output 19 channels
#1 fasta tuple
meta map

Groovy Map containing sample information e.g. [ id:'test', single_end:false]
results_*/*.fasta file

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

 *.{fasta}
#2 folder tuple
meta map

Groovy Map containing sample information e.g. [ id:'test', single_end:false]
*/ directory

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

 */
#3 dnacomp tuple
meta map

Groovy Map containing sample information e.g. [ id:'test', single_end:false]
results_*/dnacomp.txt file

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

 dnacomp.txt
#4 rescaled tuple
meta map

Groovy Map containing sample information e.g. [ id:'test', single_end:false]
results_*/*rescaled.bam file

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

 *.{bam}
#5 versions
versions.yml file

File containing software versions

 versions.yml
#6 pctot_freq tuple
meta map

Groovy Map containing sample information e.g. [ id:'test', single_end:false]
results_*/5pCtoT_freq.txt file

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

 5pCtoT_freq.txt
#7 pgtoa_freq tuple
meta map

Groovy Map containing sample information e.g. [ id:'test', single_end:false]
results_*/3pGtoA_freq.txt file

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

 3pGtoA_freq.txt
#8 length_plot tuple
meta map

Groovy Map containing sample information e.g. [ id:'test', single_end:false]
results_*/Length_plot.pdf 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
#9 runtime_log tuple
meta map

Groovy Map containing sample information e.g. [ id:'test', single_end:false]
results_*/Runtime_log.txt file

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

 Runtime_log.txt
#10 dnacomp_genome tuple
meta map

Groovy Map containing sample information e.g. [ id:'test', single_end:false]
results_*/dnacomp_genome.csv file

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

 dnacomp_genome.csv
#11 lgdistribution tuple
meta map

Groovy Map containing sample information e.g. [ id:'test', single_end:false]
results_*/lgdistribution.txt