Description

Compare multiple runs of long read sequencing data and alignments

Input

Name (Type)
Description
Pattern

meta (map)

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

]

filelist (file)

List of all the files you want to compare, they have to be all the same filetype (either fastq, fasta, bam or Nanopore sequencing summary)

*.{fastq,fq,fna,ffn,faa,frn,fa,fasta,txt,bam}

Output

Name (Type)
Description
Pattern

versions (file)

File containing software versions

versions.yml

meta (map)

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

]

report_html (file)

Summary of all collected statistics

*NanoComp-report.html

lengths_violin_html (file)

Violin plot of the sequence lengths

*NanoComp_lengths_violin.html

log_length_violin_html (file)

Violin plot of the sequence lengths, log function applied

*NanoComp_log_length_violin.html

n50_html (file)

Bar plot of N50 sequence length per sample

*NanoComp_N50.html

number_of_reads_html (file)

Bar plot of number of reads per sample

*NanoComp_number_of_reads.html

overlay_histogram_html (file)

Histogram of all read lengths per sample

*NanoComp_OverlayHistogram.html

overlay_histogram_normalized_html (file)

Normalized histogram of all read lengths per sample

*NanoComp_OverlayHistogram_Normalized.html

overlay_log_histogram_html (file)

Histogram of all read lengths per sample, log function applied

*NanoComp_OverlayLogHistogram.html

overlay_log_histogram_normalized_html (file)

Normalized histogram of all read lengths per sample, log function applied

*NanoComp_OverlayLogHistogram_Normalized.html

total_throughput_html (file)

Barplot comparing throughput in bases

*NanoComp_total_throughput.html

quals_violin_html (file)

Violin plot of base qualities, only for bam, fastq and sequencing summary input

*NanoComp_quals_violin.html

overlay_histogram_identity_html (file)

Histogram of perfect reference identity, only for bam input

*NanoComp_OverlayHistogram_Identity.html

overlay_histogram_phredscore_html (file)

Histogram of phred scores, only for bam input

*NanoComp_OverlayHistogram_PhredScore.html

percent_identity_violin_html (file)

Violin plot comparing perfect reference identity, only for bam input

*NanoComp_percentIdentity_violin.html

active_pores_over_time_html (file)

Scatter plot of active pores over time, only for sequencing summary input

*NanoComp_ActivePoresOverTime.html

cumulative_yield_plot_gigabases_html (file)

Scatter plot of cumulative yield, only for sequencing summary input

*NanoComp_CumulativeYieldPlot_Gigabases.html

sequencing_speed_over_time_html (file)

Scatter plot of sequencing speed over time, only for sequencing summary input

*NanoComp_sequencing_speed_over_time.html

stats_txt (file)

txt file with basic statistics

*NanoStats.txt
maintainer
Github user paulwolk
get in touch
Ask a question on Slack Open an issue on GitHub

Tools

nanocomp
MIT License

Compare multiple runs of long read sequencing data and alignments

github.com/wdecoster/nanocomp