diff --git a/docs/images/mqc_fastqc_adapter.png b/docs/images/mqc_fastqc_adapter.png deleted file mode 100755 index 361d0e4..0000000 Binary files a/docs/images/mqc_fastqc_adapter.png and /dev/null differ diff --git a/docs/images/mqc_fastqc_counts.png b/docs/images/mqc_fastqc_counts.png deleted file mode 100755 index cb39ebb..0000000 Binary files a/docs/images/mqc_fastqc_counts.png and /dev/null differ diff --git a/docs/images/mqc_fastqc_quality.png b/docs/images/mqc_fastqc_quality.png deleted file mode 100755 index a4b89bf..0000000 Binary files a/docs/images/mqc_fastqc_quality.png and /dev/null differ diff --git a/docs/images/multiqc_fastp.png b/docs/images/multiqc_fastp.png new file mode 100644 index 0000000..d2b6514 Binary files /dev/null and b/docs/images/multiqc_fastp.png differ diff --git a/docs/images/multiqc_general_stats.png b/docs/images/multiqc_general_stats.png new file mode 100644 index 0000000..55a0e26 Binary files /dev/null and b/docs/images/multiqc_general_stats.png differ diff --git a/docs/images/multiqc_mapping_stats.png b/docs/images/multiqc_mapping_stats.png new file mode 100644 index 0000000..38db711 Binary files /dev/null and b/docs/images/multiqc_mapping_stats.png differ diff --git a/docs/images/multiqc_variants_stats.png b/docs/images/multiqc_variants_stats.png new file mode 100644 index 0000000..08c1bc5 Binary files /dev/null and b/docs/images/multiqc_variants_stats.png differ diff --git a/docs/output.md b/docs/output.md index d6e3d97..12d79ab 100644 --- a/docs/output.md +++ b/docs/output.md @@ -154,6 +154,29 @@ Output files * `output.raxml.bestTree` A ML tree built with RAxML-NG selected as the best after running ML * `output.raxml.support` A ML tree built with RAxML-NG with support values for branches based on bootstrapping +### MultiQC +Various quality statistics are compiled from the previous outputs using the [MultiQC](https://multiqc.info/) software: + +#### Overall Statistics +A compilation of statistics about read content, mapping and variants +![General Statistics](images/multiqc_general_stats.png) + +#### FastP Statistics + +Statistics gathered when trimming reads +![FastP Statistics](images/multiqc_fastp.png) + +#### Mapping Statistics + +Statistics gathered when mapping reads +![Mapping Statistics](images/multiqc_mapping_stats.png) + + +#### Varinat Statistics + +Statistics gathered when calling variants after filtering +![Variant Statistics](images/multiqc_variants_stats.png) + ### Pipeline information