Update docs/output.md

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

docs/output.md

@@ -284,6 +284,44 @@ You will only receive the FASTQs and `*classifiedreads.txt` file if you supply `
 
 </details>
 
+### MALT
+
+[MALT](https://software-ab.cs.uni-tuebingen.de/download/malt) is a fast replacement for BLASTX, BLASTP and BLASTN, and provides both local and semi-global alignment capabilities.
+
+<details markdown="1">
+<summary>Output files</summary>
+
+- `malt/`
+  - `<db_name>/`
+  - `<sample_id>.blastn.sam`: sparse SAM file containing alignments of each hit
+  - `<sample_id>.megan`:  summary file that can be loaded into the [MEGAN6](https://uni-tuebingen.de/fakultaeten/mathematisch-naturwissenschaftliche-fakultaet/fachbereiche/informatik/lehrstuehle/algorithms-in-bioinformatics/software/megan6/) interactive viewer. Generated by MEGAN6 companion tool `rma2info`
+  - `<sample_id>.rma6`: binary file containing all alignments and taxonomic information of hits that can be loaded into the [MEGAN6](https://uni-tuebingen.de/fakultaeten/mathematisch-naturwissenschaftliche-fakultaet/fachbereiche/informatik/lehrstuehle/algorithms-in-bioinformatics/software/megan6/) interactive viewer
+  - `<sample_id>.txt.gz`: text file containing taxonomic IDs and read counts against each taxon. Generated by MEGAN6 companion tool `rma2info`
+
+</details>
+
+The main output of MALT is the `.rma6` file format, which can be only loaded into MEGAN and it's related tools. We provide the `rma2info` text files for improved compatibility with spreadsheet programs and other programmtic data manipulation tools, however this has only limited information compared to the 'binary' RMA6 file format (the `txt` file only contains taxonomic ID and count, whereas RMA6 has taxonomic lineage information).
+
+You will only recieve the `.sam` and `.megan` files if you supply `--malt_save_reads` and/or `--malt_generate_megansummary` parameters to the pipeline.
+
+
+### MetaPhlAn3
+
+[MetaPhlAn3](https://github.com/biobakery/metaphlan) is a computational tool for profiling the composition of microbial communities (Bacteria, Archaea and Eukaryotes) from metagenomic shotgun sequencing data (i.e. not 16S) with species-level resolution via marker genes.
+
+<details markdown="1">
+<summary>Output files</summary>
+
+- `metaphlan3/`
+  - `metaphlan3_<db_name>_combined_reports.txt`: A combined profile of all samples aligned to a given database (as generated by `metaphlan_merge_tables`)
+  - `<db_name>/`
+    - `<sample_id>.biom`: taxonomic profile in BIOM format
+    - `<sample_id>.bowtie2out.txt`:  BowTie2 alignment information (can be re-used for skipping alignment when re-running MetaPhlAn3 with different parameters)
+    - `<sample_id>_profile.txt`: MetaPhlAn3 taxonomic profile including abundance estimates
+
+</details>
+
+The main taxonomic profiling file from MetaPhlAn3 is the `*_profile.txt` file. This provides the abundance estimates from MetaPhlAn3 however does not include raw counts by default. 
 ### mOTUs
 
 <details markdown="1">