For an explanation of this form, please consult the User Manual.
Only letters, numbers, underscores or hyphens - Avoid using previous names
This address will be used only to notify you about the project progress
This will be used only for informative and statistical purposes
Input reads file (FASTQ / BAM / SRA, may be packed in zip / tar.bz2)
Only Ion Torrent single-end reads are admitted (up to roughly 3M reads)
Please ensure the filename contains no spaces or strange characters
Input reads file FTP / Dropbox URL
The input file must have a supported format (see above)
Desired assembly output formats
Requesting several formats will increase the size of the results folder
Use default or custom assembly options?
Default options are optimized for Ion Torrent single-end reads
Use custom options only if the result of default assembly is poor
Minimum output contig size
This is just an output threshold and has no effect on the assembly
Minimum number of reads per contig
Number of assembly passes
Maximum number of times a contig can be rebuilt during a pass
Enforce uniform read distribution in contigs
Enforce uniform read distribution: start in pass...
Minimum read length accepted
Minimum repeat length
Clip sequences by quality before assembly
Quality clip: minimum quality threshold
Quality clip: window length
Minimum length of overlap between two sequences
Minimum score of overlap between two sequences
Consult min_score parameter in the MIRA reference manual
Minimum matching % of overlap between two sequences
Genome assembly is disabled. In order to run other modules, you must provide a set of assembled contigs.
Input contigs file (FASTA)
Reference sequence file (FASTA)
Reference sequence accession / GI number
The sequence will be automatically fetched from NCBI
Two best-scoring sequence hits per alignment, at least 500 bp, 90% identity
Two best-scoring sequence hits per alignment, at least 90% identity
Please wait while your project data is transferred.This may take quite some minutes...
IonGAP uses BLAST, Circoletto, Circos, Cortex, FastQC, genoPlotR, Mauve, MIRA, mlst, MUMmer, MvirDB, Picard, Prokka and TRAMS,
and is powered by the Teide-HPC infrastructure.