Subtype Salmonella enterica subsp. enterica serovar Heidelberg genomes using an in-silico 33 bp k-mer subtyping method developed by Genevieve Labbe et al.
Subtype Salmonella Heidelberg genome assemblies (FASTA files) and/or whole-genome sequencing reads (FASTQ files)!
If you find this tool useful, please cite as:
A robust genotyping scheme for Salmonella enterica serovar Heidelberg clones circulating in North America. Geneviève Labbé1, James Robertson2, Peter Kruczkiewicz, Chad R. Laing, Kim Ziebell, Marisa Rankin, Aleisha R. Reimer, Lorelee Tschetter, Gary Van Domselaar, Eduardo N. Taboada, Sadjia Bekal, Kimberley A. MacDonald, Linda Hoang, Linda Chui, Danielle Daignault, Durda Slavic, Frank Pollari, E. Jane Parmley, Philip Mabon, Elissa Giang, Lok Kan Lee, Jonathan Moffat, Joanne MacKinnon, Benjamin M. Hetman, Roger Johnson3, John H.E. Nash4. [Manuscript in preparation]
This tool has only been tested on Linux (specifically Arch Linux). It may or may not work on OSX.
These are the external dependencies required for heidelberg_subtyping:
- Python (>=v3.5)
- BLAST+ (>=v2.6)
- for subtyping of FASTA input (assemblies)
- JELLYFISH (v2.0) (http://www.cbcb.umd.edu/software/jellyfish/)
- for subtyping of FASTQ input (raw reads)
Ensure that BLAST+ and/or JELLYFISH are installed and accessible in your $PATH.
Install heidelberg_subtyping from PyPI:
pip install heidelberg_subtypingOr install the latest master branch version directly from Github:
pip install git+https://github.com/peterk87/heidelberg_subtyping.git@masterIf you run heidelberg_subtyping -h, you should see the following usage statement:
usage: heidelberg_subtyping [-h] [-p forward_reads reverse_reads]
[-i fasta_path genome_name] [-D INPUT_DIRECTORY]
[-o OUTPUT_SUMMARY] [-O OUTPUT_TILE_RESULTS]
[--min-kmer-freq MIN_KMER_FREQ]
[--max-kmer-freq MAX_KMER_FREQ] [-t THREADS]
[-T TMP_DIR] [-K] [-v] [-V]
[F [F ...]]
Subtype Salmonella Heidelberg genomes using a 33bp k-mer typing scheme
Developed by Genevieve Labbe, Roger Johnson, PHAC-NML Guelph
positional arguments:
F Input genome FASTA/FASTQ files
optional arguments:
-h, --help show this help message and exit
-p forward_reads reverse_reads, --paired-reads forward_reads reverse_reads
FASTQ paired-end reads
-i fasta_path genome_name, --input-fasta-genome-name fasta_path genome_name
fasta file path to genome name pair
-D INPUT_DIRECTORY, --input-directory INPUT_DIRECTORY
directory of input fasta files (.fasta|.fa|.fna) or
FASTQ files (paired FASTQ should have same basename
with "_\d\.(fastq|fq)" postfix to be automatically
paired)
-o OUTPUT_SUMMARY, --output-summary OUTPUT_SUMMARY
Subtyping summary output path (tab-delimited)
-O OUTPUT_TILE_RESULTS, --output-tile-results OUTPUT_TILE_RESULTS
Subtyping tile matching output path (tab-delimited)
--min-kmer-freq MIN_KMER_FREQ
Min k-mer freq/coverage
--max-kmer-freq MAX_KMER_FREQ
Max k-mer freq/coverage
-t THREADS, --threads THREADS
Number of parallel threads to run analysis (default=1)
-T TMP_DIR, --tmp-dir TMP_DIR
Base temporary working directory for intermediate
analysis files
-K, --keep-tmp Keep temporary analysis files
-v, --verbose Logging verbosity level (-v == show warnings; -vvv ==
show debug info)
-V, --version show program's version number and exitheidelberg_subtyping -vv -o results.tab -O match_results.tab /path/to/SRR1002850.fastaContents of results.tab:
sample subtype all_subtypes tiles_matching_subtype are_subtypes_consistent inconsistent_subtypes n_tiles_matching_all n_tiles_matching_positive n_tiles_matching_subtype file_path
SRR1002850 2.2.2.2.1.4 2; 2.2; 2.2.2; 2.2.2.2; 2.2.2.2.1; 2.2.2.2.1.4 1037658-2.2.2.2.1.4; 3785187-2.2.2.2.1.4; 2154958-2.2.2.2.1.4 True 212 17 3 SRR1002850.fastaContents of match_results.tab:
tilename stitle pident length mismatch gapopen qstart qend sstart send evalue bitscore qlen slen seq coverage is_trunc refposition subtype is_pos_tile sample file_path
775920-2.2.2.2 NODE_3_length_511571_cov_26.9963_ID_5 100.0 33 0 0 1 33 475240 475272 1.5e-11 62.1 33 511571 GTTCAGGTGCTACCGAGGATCGTTTTTGGTGCG 1.0 False 775920 2.2.2.2 True SRR1002850 SRR1002850.fasta
negative3113857-1.2 NODE_4_length_474326_cov_28.1591_ID_7 100.0 33 0 0 1 33 84804 84836 1.5e-11 62.1 33 474326 TTCATGACGTCATCCCAGTCTTTTTCCGTGAAA 1.0 False negative3113857 1.2 False SRR1002850 SRR1002850.fasta
negative3159204-2.2.1.1.3 NODE_4_length_474326_cov_28.1591_ID_7 100.0 33 0 0 1 33 130145 130177 1.5e-11 62.1 33 474326 CCGCCTCGCCAACCTGCGGCGGAGTCGCGAGCT 1.0 False negative3159204 2.2.1.1.3 False SRR1002850 SRR1002850.fasta
negative3187428-2.2.3.1.1 NODE_4_length_474326_cov_28.1591_ID_7 100.0 33 0 0 1 33 158369 158401 1.5e-11 62.1 33 474326 CTTTATCAGCGCGCAGTGTCCCATTCCATCATC 1.0 False negative3187428 2.2.3.1.1 False SRR1002850 SRR1002850.fasta
negative3200083-2.1 NODE_4_length_474326_cov_28.1591_ID_7 100.0 33 0 0 1 33 171024 171056 1.5e-11 62.1 33 474326 ACCCGGTCTACCGCAAAATGGAAAGCGATATGC 1.0 False negative3200083 2.1 False SRR1002850 SRR1002850.fasta
negative3204925-2.2.3.1.5 NODE_4_length_474326_cov_28.1591_ID_7 100.0 33 0 0 1 33 175866 175898 1.5e-11 62.1 33 474326 CTCGCTGGCAAGCAGTGCGGGTACTATCGGCGG 1.0 False negative3204925 2.2.3.1.5 False SRR1002850 SRR1002850.fasta
negative3230678-2.2.2.1.1.1 NODE_4_length_474326_cov_28.1591_ID_7 100.0 33 0 0 1 33 201619 201651 1.5e-11 62.1 33 474326 AGCGGTGCGCCAAACCACCCGGAATGATGAGTG 1.0 False negative3230678 2.2.2.1.1.1 False SRR1002850 SRR1002850.fasta
negative3233869-2.1.1.1.1 NODE_4_length_474326_cov_28.1591_ID_7 100.0 33 0 0 1 33 204810 204842 1.5e-11 62.1 33 474326 CAGCGCTGGTATGTGGCTGCACCATCGTCATTA 1.0 False negative3233869 2.1.1.1.1 False SRR1002850 SRR1002850.fasta
negative3254229-2.2.3.1.3 NODE_4_length_474326_cov_28.1591_ID_7 100.0 33 0 0 1 33 225170 225202 1.5e-11 62.1 33 474326 CGCCACCACGCGGTTAGCGTCACGCTGACATTC 1.0 False negative3254229 2.2.3.1.3 False SRR1002850 SRR1002850.fastaheidelberg_subtyping -vv -t 4 -o results.tab -O match_results.tab -p SRR5646583_1.fastq SRR5646583_2.fastqContents of results.tab:
sample subtype all_subtypes tiles_matching_subtype are_subtypes_consistent inconsistent_subtypes n_tiles_matching_all n_tiles_matching_positive n_tiles_matching_subtype file_path
SRR5646583 2.2.1.1.1.1 2; 2.2; 2.2.1; 2.2.1.1; 2.2.1.1.1; 2.2.1.1.1.1 1983064-2.2.1.1.1.1; 4211912-2.2.1.1.1.1; 4568600-2.2.1.1.1.1 True 212 21 3 SRR5646583_1.fastq; SRR5646583_2.fastqContents of match_results.tab:
seq freq sample file_path tilename is_pos_tile subtype refposition is_kmer_freq_okay
ACGGTAAAAGAGGACTTGACTGGCGCGATTTGC 68 SRR5646583 SRR5646583_1.fastq; SRR5646583_2.fastq 21097-2.2.1.1.1 True 2.2.1.1.1 21097 True
AACCGGCGGTATTGGCTGCGGTAAAAGTACCGT 77 SRR5646583 SRR5646583_1.fastq; SRR5646583_2.fastq 157792-2.2.1.1.1 True 2.2.1.1.1 157792 True
CCGCTGCTTTCTGAAATCGCGCGTCGTTTCAAC 67 SRR5646583 SRR5646583_1.fastq; SRR5646583_2.fastq 293728-2.2.1.1 True 2.2.1.1 293728 True
GAATAACAGCAAAGTGATCATGATGCCGCTGGA 91 SRR5646583 SRR5646583_1.fastq; SRR5646583_2.fastq 607438-2.2.1 True 2.2.1 607438 True
CAGTTTTACATCCTGCGAAATGCGCAGCGTCAA 87 SRR5646583 SRR5646583_1.fastq; SRR5646583_2.fastq 691203-2.2.1.1 True 2.2.1.1 691203 True
CAGGAGAAAGGATGCCAGGGTCAACACGTAAAC 33 SRR5646583 SRR5646583_1.fastq; SRR5646583_2.fastq 944885-2.2.1.1.1 True 2.2.1.1.1 944885 True
GCGAACTGGCGAAACGCCTTGGCGTGGAACAAC 77 SRR5646583 SRR5646583_1.fastq; SRR5646583_2.fastq 1047714-2.2.1.1.1 True 2.2.1.1.1 1047714 True
ACAACACCGGGGTGGAGGCGCTGATTGTGCAGG 1 SRR5646583 SRR5646583_1.fastq; SRR5646583_2.fastq 1697637-2.2.2.2.2.1 True 2.2.2.2.2.1 1697637 False
GCCTGCGTTCAGTCGCTTGGGCGATATGCTGGA 65 SRR5646583 SRR5646583_1.fastq; SRR5646583_2.fastq 1983064-2.2.1.1.1.1 True 2.2.1.1.1.1 1983064 Trueheidelberg_subtyping -vv --threads <n_cpu> -o results.tab -O match_results.tab -D /path/to/fastas_or_fastqs/heidelberg_subtyping will only attempt to analyze the FASTA/FASTQ files within the specified directory and will not descend into any subdirectories!
Copyright 2017 Public Health Agency of Canada
Distributed under the GNU Public License version 3.0