7. Usage

Mikado is composed of four different programs (configure, prepare, serialise, pick) which have to be executed serially to go from an ensemble of different assemblies to the final dataset. In addition to these core programs, Mikado provides a utility to compare annotations, similarly to CuffCompare and ParsEval (compare), and various other minor utilities to perform operations such as extracting regions from a GFF, convert between different gene annotation formats, etc.

7.1. Mikado pipeline stages

• 7.1.1. Mikado configure
• 7.1.2. Mikado prepare
• 7.1.3. Mikado serialise
• 7.1.4. Mikado pick

The Mikado pipeline is composed of four different stages, that have to be executed serially:

1. Mikado configure, for creating the configuration file that will be used throughout the run.
2. Mikado prepare, for collapsing the input assemblies into a single file. After this step, it is possible to perform additional analyses on the data such as TransDecoder (highly recommended), Portcullis, or BLAST.
3. Mikado serialise, to gather all external data into a single database.
4. Mikado pick, to perform the actual selection of the best transcripts in each locus.

7.2. Compare

• 7.2.1. Compare

Mikado also comprises a dedicated utility, Mikado compare, to assess the similarity between two annotations.

7.3. Daijin

• 7.3.1. The Daijin pipeline for driving Mikado

Mikado provides a pipeline manager, Daijin, to align and assemble transcripts with multiple methods and subsequently choose the best assemblies among the options. The pipeline is implemented using Snakemake [Snake].

7.4. Miscellaneous utilities

• 7.4.1. Mikado miscellaneous scripts
  • 7.4.1.1. awk_gtf
  • 7.4.1.2. class_codes
  • 7.4.1.3. convert
  • 7.4.1.4. grep
  • 7.4.1.5. merge_blast
  • 7.4.1.6. metrics
  • 7.4.1.7. stats
  • 7.4.1.8. trim
• 7.4.2. Included scripts
  • 7.4.2.1. add_transcript_feature_to_gtf.py
  • 7.4.2.2. align_collect.py
  • 7.4.2.3. asm_collect.py
  • 7.4.2.4. bam2gtf.py
  • 7.4.2.5. class_run.py
  • 7.4.2.6. getFastaFromIds.py
  • 7.4.2.7. gffjunc_to_bed12.py
  • 7.4.2.8. grep.py
  • 7.4.2.9. merge_junction_bed12.py
  • 7.4.2.10. remove_from_embl.py
  • 7.4.2.11. sanitize_blast_db.py
  • 7.4.2.12. split_fasta.py
  • 7.4.2.13. trim_long_introns.py

Finally, Mikado provides some dedicated utilities to perform common tasks.

• Some of the utilities are integral to the Mikado suite and can be accessed as subcommands of Mikado. These utilities comprise programs to calculate annotation statistics, retrieve or exclude specific loci from a file, etc.
• Other utilities are provided as stand-alone scripts; while some of them directly depend on the Mikado library, this is not necessarily the case for them all.