Compare multiple runs of long read sequencing data and alignments
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false]
filelist{:bash}
: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}
report_html{:bash}
*NanoComp-report.html{:bash}
Summary of all collected statistics
*NanoComp-report.html
lengths_violin_html{:bash}
*NanoComp_lengths_violin.html{:bash}
Violin plot of the sequence lengths
*NanoComp_lengths_violin.html
log_length_violin_html{:bash}
*NanoComp_log_length_violin.html{:bash}
Violin plot of the sequence lengths, log function applied
*NanoComp_log_length_violin.html
n50_html{:bash}
*NanoComp_N50.html{:bash}
Bar plot of N50 sequence length per sample
*NanoComp_N50.html
number_of_reads_html{:bash}
*NanoComp_number_of_reads.html{:bash}
Bar plot of number of reads per sample
*NanoComp_number_of_reads.html
overlay_histogram_html{:bash}
*NanoComp_OverlayHistogram.html{:bash}
Histogram of all read lengths per sample
*NanoComp_OverlayHistogram.html
overlay_histogram_normalized_html{:bash}
*NanoComp_OverlayHistogram_Normalized.html{:bash}
Normalized histogram of all read lengths per sample
*NanoComp_OverlayHistogram_Normalized.html
overlay_log_histogram_html{:bash}
*NanoComp_OverlayLogHistogram.html{:bash}
Histogram of all read lengths per sample, log function applied
*NanoComp_OverlayLogHistogram.html
overlay_log_histogram_normalized_html{:bash}
*NanoComp_OverlayLogHistogram_Normalized.html{:bash}
Normalized histogram of all read lengths per sample, log function applied
*NanoComp_OverlayLogHistogram_Normalized.html
total_throughput_html{:bash}
*NanoComp_total_throughput.html{:bash}
Barplot comparing throughput in bases
*NanoComp_total_throughput.html
quals_violin_html{:bash}
*NanoComp_quals_violin.html{:bash}
Violin plot of base qualities, only for bam, fastq and sequencing summary input
*NanoComp_quals_violin.html
overlay_histogram_identity_html{:bash}
*NanoComp_OverlayHistogram_Identity.html{:bash}
Histogram of perfect reference identity, only for bam input
*NanoComp_OverlayHistogram_Identity.html
overlay_histogram_phredscore_html{:bash}
*NanoComp_OverlayHistogram_PhredScore.html{:bash}
Histogram of phred scores, only for bam input
*NanoComp_OverlayHistogram_PhredScore.html
percent_identity_violin_html{:bash}
*NanoComp_percentIdentity_violin.html{:bash}
Violin plot comparing perfect reference identity, only for bam input
*NanoComp_percentIdentity_violin.html
active_pores_over_time_html{:bash}
*NanoComp_ActivePoresOverTime.html{:bash}
Scatter plot of active pores over time, only for sequencing summary input
*NanoComp_ActivePoresOverTime.html
cumulative_yield_plot_gigabases_html{:bash}
*NanoComp_CumulativeYieldPlot_Gigabases.html{:bash}
Scatter plot of cumulative yield, only for sequencing summary input
*NanoComp_CumulativeYieldPlot_Gigabases.html
sequencing_speed_over_time_html{:bash}
*NanoComp_sequencing_speed_over_time.html{:bash}
Scatter plot of sequencing speed over time, only for sequencing summary input
*NanoComp_sequencing_speed_over_time.html
stats_txt{:bash}
*NanoStats.txt{:bash}
txt file with basic statistics
*NanoStats.txt
versions{:bash}
versions.yml{:bash}
File containing software versions
versions.yml
