Add output docs

Author: jfy133

docs/output.md

@@ -10,20 +10,65 @@
     - [Secondary Output Directories](#secondary-output-directories)
   - [MultiQC Report](#multiqc-report)
     - [General Stats Table](#general-stats-table)
+      - [Background](#background)
+      - [Table](#table)
     - [FastQC](#fastqc)
+      - [Background](#background-1)
+      - [Sequence Counts](#sequence-counts)
+      - [Sequence Quality Histograms](#sequence-quality-histograms)
+      - [Per Sequence Quality Scores](#per-sequence-quality-scores)
+      - [Per Base Sequencing Content](#per-base-sequencing-content)
+      - [Per Sequence GC Content](#per-sequence-gc-content)
+      - [Per Base N Content](#per-base-n-content)
+      - [Sequence Duplication Levels](#sequence-duplication-levels)
+      - [Overrepresented sequences](#overrepresented-sequences)
+      - [Adapter Content](#adapter-content)
     - [FastP](#fastp)
+      - [Background](#background-2)
+      - [GC Content](#gc-content)
     - [AdapterRemoval](#adapterremoval)
+      - [Background](#background-3)
+      - [Retained and Discarded Reads Plot](#retained-and-discarded-reads-plot)
+      - [Length Distribution Plot](#length-distribution-plot)
     - [Bowtie2](#bowtie2)
+      - [Background](#background-4)
+      - [Single/Paired-end alignments](#singlepaired-end-alignments)
     - [MALT](#malt)
+      - [Background](#background-5)
+      - [Metagenomic Mappability](#metagenomic-mappability)
+      - [Taxonomic assignment success](#taxonomic-assignment-success)
     - [Kraken](#kraken)
+      - [Background](#background-6)
+      - [Top Taxa](#top-taxa)
     - [Samtools](#samtools)
+      - [Background](#background-7)
+      - [Flagstat Plot](#flagstat-plot)
     - [DeDup](#dedup)
+      - [Background](#background-8)
+      - [DeDup Plot](#dedup-plot)
     - [Picard](#picard)
+      - [Background](#background-9)
+      - [Mark Duplicates](#mark-duplicates)
     - [Preseq](#preseq)
+      - [Background](#background-10)
+      - [Complexity Curve](#complexity-curve)
     - [DamageProfiler](#damageprofiler)
+      - [Background](#background-11)
+      - [Misincorporation Plots](#misincorporation-plots)
+      - [Length Distribution](#length-distribution)
     - [QualiMap](#qualimap)
+      - [Background](#background-12)
+      - [Coverage Histogram](#coverage-histogram)
+      - [Cumulative Genome Coverage](#cumulative-genome-coverage)
+      - [GC Content Distribution](#gc-content-distribution)
     - [Sex.DetERRmine](#sexdeterrmine)
+      - [Background](#background-13)
+      - [Relative Coverage](#relative-coverage)
+      - [Read Counts](#read-counts)
     - [MultiVCFAnalyzer](#multivcfanalyzer)
+      - [Background](#background-14)
+      - [Summary metrics](#summary-metrics)
+      - [Call statistics barplot](#call-statistics-barplot)
   - [Output Files](#output-files)
 
 ## Introduction
@@ -682,7 +727,7 @@ Each module has it's own output directory which sit alongside the `MultiQC/` dir
 - `nuclear_contamination/` this contains the output of the nuclear contamination processes. The directory contains one `*.X.contamination.out` file per individual, as well as `nuclear_contamination.txt` which is a summary table of the results for all individual. `nuclear_contamination.txt` contains a header, followed by one line per individual, comprised of the Method of Moments (MOM) and Maximum Likelihood (ML) contamination estimate (with their respective standard errors) for both Method1 and Method2.
 - `bedtools/` this contains two files as the output from bedtools coverage. One file contains the 'breadth' coverage (`*.breadth.gz`). This file will have the contents of your annotation file (e.g. BED/GFF), and the following subsequent columns: no. reads on feature, # bases at depth, length of feature, and % of feature. The second file (`*.depth.gz`), contains the contents of your annotation file (e.g. BED/GFF), and an additional column which is mean depth coverage (i.e. average number of reads covering each position).
 - `metagenomic_classification/` This contains the output for a given metagenomic classifier.
-  - Malt will contain RMA6 files that can be loaded into MEGAN6 or MaltExtract for phylogenetic visualisation of read taxonomic assignments and aDNA characteristics respectively. Additional a `malt.log` file is provided which gives additional information such as run-time, memory usage and per-sample statistics of numbers of alignments with taxonomic assignment etc.
+  - Malt will contain RMA6 files that can be loaded into MEGAN6 or MaltExtract for phylogenetic visualisation of read taxonomic assignments and aDNA characteristics respectively. Additional a `malt.log` file is provided which gives additional information such as run-time, memory usage and per-sample statistics of numbers of alignments with taxonomic assignment etc. This will also include gzip SAM files if requested.
   - Kraken will contain the Kraken output and report files, as well as a merged Taxon count table.
 - `maltextract/` this will contain a `results` directory in which contains the output from MaltExtract - typically one folder for each filter type, an error and a log file. The characteristics of each node (e.g. damage, read lengths, edit distances - each in different txt formats) can be seen in each sub-folder of the filter folders. Output can be visualised either with the [HOPS postprocessing script](https://github.com/rhuebler/HOPS) or [MEx-IPA](https://github.com/jfy133/MEx-IPA)
 - `consensus_sequence/` this contains three FASTA files from VCF2Genome, of a consensus sequence based on the reference FASTA with each sample's unique modifications. The main FASTA is a standard file with bases not passing the specified thresholds as Ns. The two other FASTAS (`_refmod.fasta.gz`) and (`_uncertainity.fasta.gz`) are IUPAC uncertainty codes (rather than Ns) and a special number-based uncertainty system used for other downstream tools, respectively.