Home

Services

Instructions

Output

Article abstract

snpTree 1.1 Usage Instructions

---

To generate phylogenetic tree from SNPs using the snpTree web-server you need to follow the following 5 steps:

1. Upload the files of the isolates which you want to make SNPs tree.

To input the files, upload multiple FASTQ or FASTA files or uploasd SNPs data in vcf format on your local disk by using the applet as shown in the images at the bottom of the page. Click Browse to input your genome files and click Upload to upload the files
The snpTree web-server can support unassemble short sequence reads (single end or paired end reads) in FASTQ format, support assemble genomes or contigs in FASTA format and also support SNPs data in vcf format: Below, the number and format of the files that must be uploaded is specified.

1.1 - Paired end reads

SNPs tree from paired end reads obtained by any sequencing technologies that generate paired end reads in FASTQ format.
Supported file formats: FASTQ
option: Paired end reads
In this case you will need to upload an even number of files in the supported format.

1.2 - Single end reads

SNPs tree from single end reads obtained by any sequencing technologies that generate single end reads in FASTQ format.
Supported file formats: FASTQ
option: Single end reads
In this case you will need to upload an odd or even number of files in the supported format.

1.3 - Assembled Genomes/Contigs

"Assembled Genome/Contigs" is defined as one or several contigs in one FASTA file (one entry per contig) regardsless of the type of short sequence reads used to produce the genome/contigs. The input sequence must be in one-letter nucleotide code. The allowed alphabet (not case sensitive) is the following:

A C G T and N (unknown)

Supported file formats: FASTA
option: Assembled Genomes
In this case you will need to upload an odd or even number of files in the supported format.

1.4 - SNPs files in vcf format

VCF is a text file format (most likely stored in a compressed manner). It contains meta-information lines, a header line, and then data lines each containing information about a position in the genome. VCF file is one of the ouput files that will be generated on the output page of snpTree web-server.
Example of vcf file can be seen (here)
Supported file formats: VCF
option: SNPs files (vcf)
In this case you will need to upload an odd or even number of vcf files

Note: all vcf files need to generated from the same reference genome.

2. Upload or select the reference genome for SNPs identification

Upload: Click the blue text "Upload Reference Genome". You will now be able to upload a file from your own computer as reference.

Select: Use the drop down list to select the reference genome in which consists of more than 1,600 completed bacterial genomes from NCBI.

• Note: all reference genomes contain only the chromosome, it does not contain any plastmids.

3. Select type of input genomes

See section 1 for more details on supported sequence types and supported file formats.

4. Select SNPs calling parameters (optional)

There are three parameters for SNPs calling. (You can leave them as default).

4.1 - minimum coverage

Minimum coverage is the minimum limit to read depth that one will accept for SNP calls. This value is depends on the sequence coverage of your sample.
This parameter is only for raw reads
The default is 10.

4.2 - minimum distance between SNPs (prune)

Minimum distance between SNPs or prune is the distance in the given number of basepair between any SNPs for example if prune = 20 means that if there are variant calls within 20 bp of each other they will be filtered out. These are often errors caused by indels in the alignment.
This parameter is for raw reads and assemble genomes/contigs
The default is 10 bp.

4.3 - minimum distance to end of sequence

Minimum distance to end of sequence is the given number of basepair from a reference sequence end that SNPs have been found. These SNPs will be filtered out.
This parameter is only for assemble genomes/contigs
The default is 0 bp.

5. Submit the job

Click on the "Submit" button. The status of your job (either queued or running) will be displayed and constantly updated until it terminates and the server output page appears in your browser. You also have the option to input your email and be notified as soon as your the results are ready.
The e-mail message will contain the URL under which the results are stored; they will remain on the server for 48 hours for you to collect them.
IMPORTANT: In order to make the URL visible on your browser. You will have to copy and paste the URL in your browser like the example below;

www.cbs.dtu.dk/URL

An overview of the upload