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ESSENTIALS: Transposon insertion sequencing analysis
(1/4) Select genome and upload configuration file

ESSENTIALS: Transposon insertion sequencing analysis logo
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Aldert Zomer1,2, Peter Burghout1, Hester Bootsma1, Peter Hermans1 and Sacha van Hijum2

1Laboratory of Pediatric Infectious Diseases
2Centre for Molecular and Biomolecular Informatics, Bacterial Genomics

To identify microbial genes essential for growth of micro-organisms, an insertion knockout strategy that allows rapid identification of disrupted genes can be used. Methods, such as Tn-Seq, INseq and TraDIS employ next generation sequencing methods to sample flanking sequences of transposon insertions. ESSENTIALS maps these sequence reads and generates profiles of these libraries. Genes that are not detected in the knockout library are likely essential for growth if a sufficiently large knockout library is used. In addition, by comparing the profiles of a library that was exposed to different environments, conditionally essential genes can also be detected.

If you make use of this software for your research please cite:
Zomer A, Burghout P, Bootsma HJ, Hermans PWM, van Hijum SAFT (2012) ESSENTIALS: Software for Rapid Analysis of High Throughput Transposon Insertion Sequencing Data. PLoS ONE 7(8):e43012. Epub 2012 Aug 10.


Data Submission Form
Use this form to submit a configuration file and a genbank formatted genome file.
ESSENTIALS understands (compressed) fasta, fastq, scarf, export and solid read files. For detection of conditionally essential genes include target and control samples. If your sequence reads do not contain barcodes or transposon sequences that have to be trimmed and splitted, please use N as a sequence in the config file.
A manual with all the settings explained in detail can be downloaded here (pdf)
Your data will be stored on our server for up to three weeks and will be kept confidential.
Source codes of the perl and R scripts are available on request.

Please do not use LOESS correction if you have less than 2000 mutants. This might cause artefacts or even a run failure.

Template genome
Finished genome


Alternatively, upload a genbank file if your genome is not in the list
Genbank file


Run mode

Upload configfile
Upload configuration file (tab delimited matrix, see example and manual)





Create config file
Enter number of samples, in the next page the sample descriptions can be provided by the user



Run in Demo mode on in house generated S. pneumoniae R6 data



Optionally, upload a profile with favorite parameter settings here
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