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On this page
  • Data download options
  • Sequencer Types
  • Illumina
  • Nanopore
  • Sample Types
  • FASTA
  • FASTQ
  • FASTQ (compressed)
  • How to retrieve genome sequence data
  1. Protocols
  2. Genome Identification

Prepare Samples

Data download options

Uploading your genome sequencing data to our private service is a straightforward process, but there are a few steps to ensure everything goes smoothly. First, we must prepare the samples for upload.

Sample types are split between pre-assembled genomes as FASTA and unassembled genomes in FASTQ format. Both, illumina- and Nanopore-sequenced files are compatible with this service. Compressed (gunzip) sequences can be uploaded for speed and convenience.

Sequencer Types

Illumina

Illumina sequencing generates short, high-quality reads that are ideal for assembling high-accuracy genomes. This type of data is often provided in FASTQ format.

Illumina HiSeq, MiSeq, NextSeq, NovaSeq

Nanopore

Nanopore sequencing produces long reads that can span entire genes or large genomic regions, making it useful for resolving complex regions of the genome. Nanopore data is also typically provided in FASTQ format and is valuable for assemblies where read length is crucial.

Oxford Nanopore MinION, GridION, PromethION

Sample Types

Depending on the sequencing machine, settings used, and post-processing, samples will produce different types of files.

FASTA

FASTA files contain already assembled genomic sequences, where the reads have been combined into longer contiguous sequences (contigs or scaffolds).

FASTQ

FASTQ files include raw sequencing reads with associated quality scores, providing detailed information for assembly or alignment processes.

FASTQ (compressed)

Compressed FASTQ files (gzipped) reduce file size for faster upload while still preserving the raw sequencing reads and quality scores.

How to retrieve genome sequence data

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Last updated 8 months ago

Let's identify your isolate using or practice with the , provided.

⚗️
your isolate genome data
example files

Private Samples

Locally stored genome sequence files in FASTA or FASTQ (compressed and uncompressed) formats. Illumina and Nanopore sequence files are compatible.

Public Samples

Retrieve public genome sequence files in FASTA or FASTQ (compressed and uncompressed) formats. Illumina and Nanopore sequence files are compatible.