Input and Output

• Input files
  • Paired-end reads
  • Genome assemblies
• Output
  • Standard Out
• Output files
  • identified_alleles.fna
  • intermediate_outputs.txt
  • possible_mlsts.txt
  • reads_vs_all_ref_filt_sorted.bam
  • reads_vs_all_ref_filt_sorted.bam.bai
  • report.json
  • run.log

Input files

If available, we recommend using raw or trimmed reads instead of assemblies, as the extra data contained in reads is valuable for the process used by el_gato to identify sample ST. When run with reads, el_gato can use read quality and coverage information to apply quality control rules. When run using assemblies, el_gato cannot identify errors incorporated into the assembly and may report incorrect results. For example, while many isolates encode two copies of mompS, in some cases, the assembly includes only one copy of the locus. If the assembly consists of only the secondary mompS locus, el_gato will report that allele.

Pair-end reads

When running on a directory of reads, files are associated as pairs using the *_R1 *_R2 pattern i.e., filenames should be identical except for containing either "R1" or "R2" and can be .fastq or .fastq.gz format. el_gato will not process any files for which it cannot identify a pair using this pattern.

Genome assemblies

When running on a directory of assemblies, el_gato will process all files in the target directory, and no filename restrictions exist.

Output

After a run, el_gato will print the identified ST of your sample to your terminal (stdout) and write several files to the specified output directory (default: out/). el_gato creates a subdirectory for each processed sample, including five output files with specific information.

Standard out

el_gato writes the ST profile as a tab-delimited table without headings. If you run el_gato with the -e flag, it includes the headings and displays them like this:

Sample ST flaA pilE asd mip mompS proA neuA_neuAH

• The sample column contains the user-provided or inferred sample name.

• The ST column contains the sequence type of the sample. The ST column contains two kinds of values. If the identified allelic profile corresponds to a ST found in the database, el_gato provides the corresponding number. If el_gato finds no matching profile or if el_gato is unable to make a confident call for one or more alleles, then a descriptive symbol will be listed. See table below for symbol meanings.

• flaA, pilE, asd, mip, mompS, proA, and neuA/neuAh columns contain the respective allele numbers for each locus

• For each locus, if an exact allele match is found in the database, the corresponding allele number is reported. If an exact match is not identified in the database, a descriptive symbol will be listed. See table below for symbol meanings.

Symbol	Meaning
Novel ST	Novel Sequence Type: All 7 target genes were found but not present in the profile - most likely a novel sequence type.
Novel ST*	Novel Sequence Type due to novel allele: One or multiple target genes have a novel allele found.
MD-	Missing Data: ST is unidentifiable as a result of or more of the target genes that are unidentifiable.
MA?	Multiple Alleles: ST is ambiguous due to multiple alleles that could not be resolved.
NAT	Novel Allele Type: BLAST cannot find an exact allele match - most likely a new allele.
-	Missing Data: Both percent and length identities are too low to return a match or N's in sequence.
?	Multiple Alleles: More than one allele was found and could not be resolved.

If symbols are present in the ST profile, the other output files produced by el_gato will provide information to clarify the source of the symbol.

Output files

The files included in the output directory for a sample are:

identified_alleles.fna

The nucleotide sequence of all identified alleles is written in this file. If more than one allele is determined for the same locus, they are numbered arbitrarily. Fasta headers of sequences in this file correspond to the query IDs in the BLAST output reported in the intermediate_outputs.txt file.

intermediate_outputs.txt

el_gato calls other programs to perform intermediate analyses. The outputs of those programs are provided in this file. In addition, essential log messages are also written in this file to help with troubleshooting. The following information may be contained in this file, depending on if the input is reads or assembly:

• Reads-only - Samtools coverage command output. See samtools coverage documentation for more information about headers or here.

• Reads-only - Information about the orientation of mompS sequencing primer in reads mapping to biallelic sites. See Approach subsection for more details.

• BLAST output indicating the best match for identified alleles. See BLAST output documentation for more information about headers or here.

possible_mlsts.txt

This file contains all possible ST profiles if el_gato identifies multiple possible alleles for any ST loci. In addition, if multiple mompS alleles are found, the information used to determine the primary allele is reported in this file in the "mompS_reads_support" and "mompS_reads_against" columns. mompS_reads_support indicates the number of reads associated with each allele that contains the reverse sequencing primer in the expected orientation, suggesting that this is the primary allele. mompS_reads_against indicates the number of reads containing the reverse sequencing primer in the wrong orientation and thus suggesting that this is the secondary allele. These values are used to infer which allele is the primary mompS allele, and their values can be considered to represent the confidence of this characterization. See Approach subsection for more details.

reads_vs_all_ref_filt_sorted.bam

el_gato maps the provided reads to a set of reference sequences in the el_gato db directory. The mapped reads are then used to extract the sequences present in the sample to identify the alleles and, ultimately, the ST. reads_vs_all_ref_filt_sorted.bam and its associated file reads_vs_all_ref_filt_sorted.bai contains the mapping information used by el_gato. The BAM file can be viewed using software such as IGV to understand better the data used by el_gato to make allele calls. Additionally, this file is a good starting point for investigating the cause of incorrectly resolved loci.

reads_vs_all_ref_filt_sorted.bam.bai

Index files allow programs that can read them to work with the data in the associated files.

report.json

Each sample outputs a JSON file that contains relevant information about the run, which will be included in the PDF report.

• Report Summary page: Summary of el_gato and complete ST profile for each sample included in the report.

• Definitions Overview page: ST definitions key and evidence for support of mompS allele call key.

• Paired-end reads: Locus coverage information and mompS primer information parsed by each sample.

• Assembly: BLAST hit length and sequence identity thresholds and locus location information parsed by each sample.

run.log

A detailed log of the steps taken during el_gato's running includes the outputs of any programs called by el_gato and any errors encountered. Some command outputs include headers (e.g., samtools coverage and BLAST).