RefSeq Masher - Genomic Distance

Find what NCBI RefSeq genomes most closely match your sequence data using Mash with a Mash sketch database of 54,925 NCBI RefSeq Genomes.

Source code available on Github at github.com/phac-nml/refseq_masher

matches - find the closest matching NCBI RefSeq Genomes in your input sequences

Command-line usage information:

Usage: refseq_masher matches [OPTIONS] INPUT...

  Find NCBI RefSeq genome matches for an input genome fasta file

  Input is expected to be one or more FASTA/FASTQ files or one or more
  directories containing FASTA/FASTQ files. Files can be Gzipped.

Options:
  --mash-bin TEXT                 Mash binary path (default="mash")
  -o, --output PATH               Output file path (default="-"/stdout)
  --output-type [tab|csv]         Output file type (tab|csv)
  -n, --top-n-results INTEGER     Output top N results sorted by distance in
                                  ascending order (default=5)
  -m, --min-kmer-threshold INTEGER
                                  Mash sketch of reads: "Minimum copies of
                                  each k-mer required to pass noise filter for
                                  reads" (default=8)
  -h, --help                      Show this message and exit.

Example

With the FNA.GZ file for Salmonella enterica subsp. enterica serovar Enteritidis str. CHS44:

# download sequence file
wget ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/329/025/GCF_000329025.1_ASM32902v1/GCF_000329025.1_ASM32902v1_genomic.fna.gz

# find RefSeq matches
refseq_masher -vv matches GCF_000329025.1_ASM32902v1_genomic.fna.gz

Log:

2018-01-29 11:02:13,786 INFO: Collected 1 FASTA inputs and 0 read sets [in ...refseq_masher/refseq_masher/utils.py:185]
2018-01-29 11:02:13,786 INFO: Creating Mash sketch file for ...refseq_masher/GCF_000329025.1_ASM32902v1_genomic.fna.gz [in ...refseq_masher/refseq_masher/mash/sketch.py:24]
2018-01-29 11:02:14,055 INFO: Created Mash sketch file at "/tmp/GCF_000329025.1_ASM32902v1_genomic.msh" [in ...refseq_masher/refseq_masher/mash/sketch.py:40]
2018-01-29 11:02:14,613 INFO: Ran Mash dist successfully (output length=11647035). Parsing Mash dist output [in ...refseq_masher/refseq_masher/mash/dist.py:64]
2018-01-29 11:02:15,320 INFO: Parsed Mash dist output into Pandas DataFrame with 54924 rows [in ...refseq_masher/refseq_masher/mash/dist.py:67]
2018-01-29 11:02:15,321 INFO: Deleting temporary sketch file "/tmp/GCF_000329025.1_ASM32902v1_genomic.msh" [in ...refseq_masher/refseq_masher/mash/dist.py:72]
2018-01-29 11:02:15,321 INFO: Sketch file "/tmp/GCF_000329025.1_ASM32902v1_genomic.msh" deleted! [in ...refseq_masher/refseq_masher/mash/dist.py:74]
2018-01-29 11:02:15,322 INFO: Ran Mash dist on all input. Merging NCBI taxonomic information into results output. [in ...refseq_masher/refseq_masher/cli.py:88]
2018-01-29 11:02:15,323 INFO: Fetching all taxonomy info for 5 unique NCBI Taxonomy UIDs [in ...refseq_masher/refseq_masher/taxonomy.py:35]
2018-01-29 11:02:15,325 INFO: Dropping columns with all NA values (ncol=32) [in ...refseq_masher/refseq_masher/taxonomy.py:38]
2018-01-29 11:02:15,327 INFO: Columns with all NA values dropped (ncol=11) [in ...refseq_masher/refseq_masher/taxonomy.py:40]
2018-01-29 11:02:15,327 INFO: Merging Mash results with relevant taxonomic information [in ...refseq_masher/refseq_masher/taxonomy.py:41]
2018-01-29 11:02:15,329 INFO: Merged Mash results with taxonomy info [in ...refseq_masher/refseq_masher/taxonomy.py:43]
2018-01-29 11:02:15,329 INFO: Merged taxonomic info into results output [in ...refseq_masher/refseq_masher/cli.py:90]
2018-01-29 11:02:15,329 INFO: Reordering output columns [in ...refseq_masher/refseq_masher/cli.py:91]
2018-01-29 11:02:15,331 INFO: Writing output to stdout [in ...refseq_masher/refseq_masher/writers.py:16]

Output

sample	top_taxonomy_name	distance	pvalue	matching	full_taxonomy	taxonomic_subspecies	taxonomic_species	taxonomic_genus	taxonomic_family	taxonomic_order	taxonomic_class	taxonomic_phylum	taxonomic_superkingdom	subspecies	serovar	plasmid	bioproject	biosample	taxid	assembly_accession	match_id
GCF_000329025.1_ASM32902v1_genomic	Salmonella enterica subsp. enterica serovar Enteritidis str. CHS44	0.0	0.0	400/400	Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales; Enterobacteriaceae; Salmonella; enterica; subsp. enterica; serovar Enteritidis; str. CHS44	Salmonella enterica subsp. enterica	Salmonella enterica	Salmonella	Enterobacteriaceae	Enterobacterales	Gammaproteobacteria	Proteobacteria	Bacteria	enterica	Enteritidis		PRJNA185053	SAMN01041154	702979	NZ_ALFF	./rcn/refseq-NZ-702979-PRJNA185053-SAMN01041154-NZ_ALFF-.-Salmonella_enterica_subsp._enterica_serovar_Enteritidis_str._CHS44.fna

The top match is Salmonella enterica subsp. enterica serovar Enteritidis str. CHS44 with a distance of 0.0 and 400/400 sketches matching, which is what we expected. There's other taxonomic information available in the results table that may be useful.

Legal

Written by: National Microbiology Laboratory, Public Health Agency of Canada

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this work except in compliance with the License. You may obtain a copy of the License at:

www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

Contact

Gary van Domselaar: gary.vandomselaar@phac-aspc.gc.ca