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BRC4_genome_compare_conf.md

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Compare genomes pipeline

MODULE: Bio::EnsEMBL::Pipeline::PipeConfig::BRC4_genome_compare_conf

Overview

This pipeline is used for a sequence-level comparison of an assembly with INSDC and provides a detailed report on the discrepancies. The following steps are performed:

  1. Download the files for the corresponding assembly from INSDC
  2. Retrieve metadata seq.json and fasta files from the database
  3. Compare the fasta files
    • compare the sequence ids
    • compare the sequence
    • MD5 check of the files
    • identify organellar sequences in both assemblies
  4. Report the results

Prerequisites

A registry file to connect to the database.

Example of how to create the pipeline

init_pipeline.pl Bio::EnsEMBL::Pipeline::PipeConfig::BRC4_genome_compare_conf \
  --host $HOST --port $PORT --user $USER --pass $PASS \
  --registry $REGISTRY \
  --hive_force_init 1 \
  --output_dir $OUTPUT_DIR \
  --tmp_dir temp/compare \
  --species acanthamoeba_astronyxis_gca000826245

PARAMETERS

Options Type Default value Mandatory Description
--registry file yes service that connects to the database
--pipeline_name str brc4_genome_compare optional name of the hive pipeline
--hive_force_init int yes drop and create the hive pipeline from scratch
--output_dir dir ./output optional directory to store the result
--tmp_dir dir ./tmp optional temp directory for downloaded files
--species str yes species (one or multiple) to process (production name)
--run_all int 0 yes process all the species in the registry
--email str $USER.ebi.ac.uk optional a summary is emailed when the pipeline is complete

Note: Either use --species to run one or multiple species separately or --run_all 1 for all the species in the database. Currently this pipeline is only used to compare with Genbank assembly.

RESULT

Generates 3 files:

  • report.log: A tab-delimited file containing a summary of the compared sequences between the INSDC assembly/assemblies and the database(s)

    • The report contains 13 columns:
      • species: name of the species
      • accession: GCA accession
      • seq_count_1: total number of sequences in INSDC
      • seq_count_2: total number of sequences in the database
      • num_diff_seq: the total number of sequences that differ between INSDC and the database
      • common: the total number of common sequences between INSDC and the database
      • only1: count of sequences found only in INSDC
      • only2: count of sequences found only in the database
      • max_only1: a total of the sequence length in only1
      • max_only2: a total of the sequence length in only2
      • other_locations: the total count of organellar genomes
      • summary (mismatch or identical)
      • organellar_summary

  • species_fasta_dna.map: A JSON schema file containing metadata of the common sequences

  • species_fasta_dna.log: Detailed report of mismatched sequences