Toolkit for annotation
- alignscore.txt (used in run_genblast_align)
support_classes (should be moved to https://github.com/Ensembl/ensembl-genes-api)
- exon.py
- gene.py
- gtf_adapter.py
- intron.py
- sequence.py
- transcript.py
- subsample_fastq.py
support_scripts_perl (should be re-written in python, when API has enough functionality, and added to support_scripts)
- clean_geneset.pl
- clean_utrs_and_lncRNAs.pl
- finalise_geneset.pl
- gtf_to_seq.pl
- load_gtf_ensembl.pl
- select_best_transcripts.pl
| Software | Version | URL | Required |
|---|
| Repository name | branch | URL |
|---|---|---|
| ensembl-genes | default | https://github.com/Ensembl/ensembl-genes.git |
| Repository name | branch | URL |
|---|---|---|
| ensembl | default | https://github.com/Ensembl/ensembl.git |
| ensembl-analysis | experimental/gbiab | https://github.com/Ensembl/ensembl-analysis.git |
| ensembl-variation | default | https://github.com/Ensembl/ensembl-variation.git |
python3 ensembl_anno.py -h
[-h] [--output_dir OUTPUT_DIR] --genome_file
GENOME_FILE [--num_threads NUM_THREADS] [--run_masking]
[--red_path RED_PATH] [--genblast_path GENBLAST_PATH]
[--convert2blastmask_path CONVERT2BLASTMASK_PATH]
[--makeblastdb_path MAKEBLASTDB_PATH] [--run_genblast]
[--run_busco] [--protein_file PROTEIN_FILE]
[--busco_protein_file BUSCO_PROTEIN_FILE]
[--rfam_accessions_file RFAM_ACCESSIONS_FILE]
[--run_star] [--star_path STAR_PATH]
[--max_reads_per_sample [MAX_READS_PER_SAMPLE]]
[--max_total_reads [MAX_TOTAL_READS]]
[--short_read_fastq_dir SHORT_READ_FASTQ_DIR]
[--max_intron_length [MAX_INTRON_LENGTH]]
[--run_minimap2] [--minimap2_path]
[--paftools_path PAFTOOLS_PATH]
[--long_read_fastq_dir LONG_READ_FASTQ_DIR]
[--run_augustus] [--augustus_path AUGUSTUS_PATH]
[--run_stringtie] [--run_scallop]
[--stringtie_path STRINGTIE_PATH]
[--scallop_path SCALLOP_PATH]
[--subsample_script_path SUBSAMPLE_SCRIPT_PATH]
[--samtools_path SAMTOOLS_PATH] [--finalise_geneset]
[--db_details DB_DETAILS] [--run_cmsearch] [--run_trf]
[--trf_path TRF_PATH] [--run_dust]
[--dust_path DUST_PATH] [--run_repeatmasker]
[--repeatmasker_path] [--run_trnascan]
[--trnascan_path TRNASCAN_PATH]
[--trnascan_filter_path TRNASCAN_FILTER_PATH]
[--run_cpg] [--cpg_path CPG_PATH] [--run_eponine]
[--eponine_path EPONINE_PATH] [--java_path JAVA_PATH]
[--run_full_annotation] [--run_repeats]
[--run_simple_features] [--run_sncrnas]
[--run_transcriptomic] [--run_proteins]
[--diamond_validation_db DIAMOND_VALIDATION_DB]
[--validation_type VALIDATION_TYPE]
[--load_to_ensembl_db] [--trim_fastq]
[--delete_pre_trim_fastq]
[--repeatmasker_library REPEATMASKER_LIBRARY]
[--repeatmasker_species REPEATMASKER_SPECIES]
--run_full_annotation
Includes:
--run_repeats
| Analysis | Software | Input | Output |
|---|---|---|---|
| --run_masking | red | genome_file, red_path, work_dir | <work_dir>/redt_output/mask_output/<genome_file_name>.msk |
| --run_dust | dust | genome_file, dust_path, work_dir, num_threads | <work_dir>/dust_output/<seq_region_name>.dust.gtf (per region) |
| --run_trf | trf | genome_file, trf_path, work_dir, num_threads | <work_dir>/trf_output/<seq_region_name>.trf.gtf (per region) |
--run_simple_features
| Analysis | Software | Input | Output |
|---|---|---|---|
| --run_cpg | cpg | genome_file, cpg_path, work_dir, num_threads | <work_dir>/cpg_output/<seq_region_name>.cpg.gtf (per region) |
| --run_eponine | eponine | genome_file, java_path, eponine_path, work_dir, num_threads | <work_dir>/cpg_output/<seq_region_name>.epo.gtf (per region) |
--run_sncrnas
| Analysis | Software | Input | Output |
|---|---|---|---|
| --run_trnascan | trnascan | genome_file, trnascan_path, trnascan_filter_path, work_dir, num_threads | <work_dir>/trnascan_output/<seq_region_name>.trna.gtf (per region) |
| --run_cmsearch* | cmsearch | genome_file, cmsearch_path, rfam_cm_db_path, rfam_seeds_file_path, rfam_accession_file, work_dir, num_threads | <work_dir>/rfam_output/<seq_region_name>.rfam.gtf (per region) |
*requires --rfam_accessions_file, will skip if missing
--run_transcriptomic
short-read data
| Analysis | Software | Input | Output |
|---|
long-read data
| Analysis | Software | Input | Output |
|---|
--run_proteins
| Analysis | Software | Input | Output |
|---|
--finalise_geneset
| Analysis | Software | Input | Output |
|---|
--run_repeatmasker