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Outputs Explained

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Aidan Foo edited this page Jan 12, 2022 · 1 revision

Here I will explain the outputs

Outputs Explained

Here we list the outputs of MINUUR

Host Separation

qc

fastqc fastqc report per sample of the raw unmapped sequences fastqc_trimmed fastqc report per sample of trimmed sequences trimmed_fastq trimmed fastq files

aligned_bam

If your input was a paired fastq file, this folder will output a list of coordinate sorted BAM files of your raw reads against the reference genome of your choosing.

alignment_stats (or alignment_stats_ffq)

A folder listing a simple set of alignment statistics of of your data, including reads mapped, reads unmapped and raw total sequences. There is also a concatenated .txt file of all your samples with their alignment statistics.

bam_stats (or bam_stats_ffq)

A folder listing a detailed summary of the bowtie2 alignment, generated using samtools.

Taxonomic Read Classification

kraken_out

Kraken2 classification of unmapped reads combined_report: concatenated file of all taxonomic classifications from all samples mpa_out: mpa style report of Kraken2 classifications mpa_report: mpa style report with unclassified reads report: FINISH

kraken_results

classified_summary: .txt file per sample showing proportion of reads classified and proportion of reads unclassified concatenated_kraken_summary.txt: concatenated file of kraken summaries plots: -> classified_proportions.pdf: proportion of reads classified and unclassified per sample. -> species_heatmap.pdf: log number of reads classified across species with a user provided read threshold -> genus_heatmap.pdf: log number of reads classified across genus with a user provided read threshold -> species_spatial_plot.pdf: Spatial plot of raw number of classified reads against each species -> genus_spatial_plot.pdf: Spatial plot of raw number of classified reads against each genus -> stratified_heatmap.pdf: species stratified heatmap with log number of reads

tables: summary tables classified_reads_table.txt gives the study and total number of reads classified in question. species_table_tidy.txt summarized table of species classified, number of associated reads and sample in question. kingdom_table_tidy and genus_table_tidy give the same information at these taxonomic levels.

kraken_taxon_extract: paired fastq files of user specified taxon/taxa of interest. Can be used for further analysis. e.g. isolate genome assemblies, gene calling.

bracken_reestimation

Reestimation of Kraken2 classified reads to infer taxonomic relative abundance bracken_out: .txt files with Kraken2 classified taxonomic IDs, kraken assigned reads, added reads, new estimated number of reads and fraction of total reads. concat_bracken_out: concatenated file of all samples and Bracken added reads plots: --> added_reads_plot.pdf: bar graph and bracken added reads per sample --> FINISH

metaphlan_out

MetaPhlAn3 taxonomic classifications.
bowtie2_aln .bz2 alignment files, can be used for further analysis or quickly repeating the MetaPhlAn3 taxonomic classification clean_summaries: clean taxonomic summaries with either species, genus, kingdom, the sample it originated from and relative abundance. taxa_profile: is the MetaPhlAn3 taxonomic class

Functional Read Profiling

humann_out

concatenated_humann_files: files with raw gene families (RPK), pathway abundances (RPK) and pathway coverage (0-1) concatenated across all samples. Also includes stratified and unstratified files, normalized relative abundance and gene families with relative abundance renamed with UniRef90 IDs.

plots: gene_and_path_hits_per_sample.pdf: number of hits across gene and pathway abundance profiles per sample gene_and_path_hits_per_spsecies.pdf: number of hits across gene and pathway abundance profiles per species gene_hits.pdf: number of identified genes per sample and their percentage identity to their alignments. Size of each dot denotes the number of genes identified at that specific identity threshold.

Metagenome Assembly

megahit_assm

Each directory contains the sample and assembled contigs, named final.contigs.fa.

quast_out

quast report of assmembled contigs generated from the megahit assembly. concat_transposed_report.tsv is a concatenated quast report per sample.

binning

The binning folder contains the output of checkm and metabat. checkm_out: concatenated bin statistics including N50 and L50 scores of all binned genomes. QA_out contains quality assurance per bin. metabat_out: will contain binned genomes in .fasta format. plots: -> BarChartCompletenessContamination.pdf: Flipped bar chart with sample on the y-axis and CheckM contamination & completeness score on the x-axis. Light blue bar = completeness and dark blue bar = contamination. -> CompletenessVsContam_Per_Sample.pdf: Dot plot showing completeness and contamination of each bin colour coded by sample (note this figure is best suited where samples are <10). Orange line >= completeness 50%, green line >= completeness >= 80%

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