The Structure of a Project Configuration File

Section [General]

[General]
output_directory = /home/kakapo/kakapo-output
project_name = kakapo-prj-01
entrez_api_key = xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
run_rcorrector = Yes
run_inter_pro_scan = No
prepend_assembly_name_to_sequence_name = Yes
kraken_2_confidence = 0.20
requery_after = 7
use_colors = Yes

• output_directory: a path to a directory where kakapo should place all of its output.

• project_name: a short (hopefully meaningful) name for the analysis. kakapo will create a subdirectory with this name where a bunch of project-specific output will be stored (log files, backups of the configuration files used, assembled sequences, etc): [output_directory]/02-project-specific/[project_name].

• entrez_api_key: kakapo will make use of the public resources on GenBank. GenBank users are allowed 3 requests/second without an API key. With an API key, the limit is increased to 10 requests/second. You will need to generate the key here: https://www.ncbi.nlm.nih.gov/account/settings

• run_rcorrector: if set to Yes, the reads will be processed by Rcorrector.

• run_inter_pro_scan: if set to Yes, the translated CDS sequences found by kakapo will be submitted for functional annotation by InterProScan to https://www.ebi.ac.uk/interpro/search/sequence.

• prepend_assembly_name_to_sequence_name: if set to Yes, will prepend sample name to the assembled isoform names. The sample name is derived based on the type of input:

  • SRA: GenBank metadata.
  • FASTQ: file name.
  • FASTA (user-provided assembly): file name.

  if set to No, unaltered names produced by SPAdes will be used in kakapo output. I highly discourage setting this option to No when more than one sample is being analyzed.

• kraken_2_confidence: this should be set to a value between 0 and 1. I find that a value of 0.20 works quite well. Higher confidence values will reduce the number of reads classified (filtered out), and lower values will increase it. See discussion here, for more guidance.

• requery_after: Do not search GenBank and/or Pfam if the search was performed already and the results are less than this many days old.

• use_colors: if set to Yes, adds color to the log messages in the terminal, may not look great on light terminal backgrounds.

[Target filters]
# Allow other start codons, in addition to AUG.
# A set of appropriate start codons will be chosen
# using GenBank taxonomical classification.
#
# If allow_non_aug_start_codon is set to No,
# allow_missing_start_codon will have no effect
allow_non_aug_start_codon = No

# Annotate ORFs even if the start codon is missing.
#
# For allow_missing_start_codon to have any effect,
# allow_non_aug_start_codon must be set to Yes
allow_missing_start_codon = No

# Annotate ORFs even if the stop codon is missing.
allow_missing_stop_codon = No

[Query taxonomic group]
# Choose between: animals, archaea, bacteria, fungi, plants, viruses
plants

[Target SRA accessions]
# SRR7829961
# SRR23214014
# ...

[Target FASTQ files]
# pe_001 = /home/kakapo/kakapo-input/fastq/Solanum_chilense_sample1_R*.fastq.gz
# pe_002 = /home/kakapo/kakapo-input/fastq/Solanum_chilense_sample2_R*.fastq
# pe_003 = /home/kakapo/kakapo-input/fastq/Solanum_chilense_sample3_R*.fq.gz
# ...

# se_001 = /home/kakapo/kakapo-input/fastq/Solanum_chilense_sample4_R1.fastq.gz
# se_002 = /home/kakapo/kakapo-input/fastq/Solanum_chilense_sample5_R1.fastq
# se_003 = /home/kakapo/kakapo-input/fastq/Solanum_chilense_sample6_R1.fq
# ...

[Target assemblies: FASTA files (DNA)]
# /home/kakapo/kakapo-input/assemblies/Matucana_madisoniorum_HBG13.fasta
# ...

[Bowtie2 filter order]
# cactus_virus_x = /home/kakapo/kakapo-input/reference_genomes/cactus_virus_x.fasta
# plastid
# mitochondrion
# ...

[Kraken2 filter order]
# 16S_Silva132
# 16S_Silva138
# viral
# mitochondrion
# plastid
# mitochondrion_and_plastid
# minikraken_8GB_2020-03-12

[BLAST SRA/FASTQ]
evalue = 1e-5
max_hsps = 10000
qcov_hsp_perc = 1
best_hit_overhang = 0.05
best_hit_score_edge = 0.25
max_target_seqs = 1000000

# If any of these settings are present in the
# search strategies files, they will be overwritten
# for each search strategy
[BLAST assemblies]
evalue = 1e-20
max_hsps = 4
qcov_hsp_perc = 70
best_hit_overhang = 0.15
best_hit_score_edge = 0.15
max_target_seqs = 500