Run multiple module in one job

AssemblyMapper

Step1: Uploading reference genome or choose online resource

Select reference genome online:

Or, upload your own reference genome:

Upload reference genome

Reference genome file (FASTA format)

Step2: Uploading contigs

Note that the contig level assembly should be phased .

Upload contigs file:

Upload contigs

Contigs file (FASTA format)

Step3: Setting algorithm parameters

Hover the mouse over the parameter label to see detailed description.
You may input values outside the range directly in the input box, but may not receive satisfactory result.

Contigs shorter than INT (bp) will
be removed, default: 50000

Min Contigs Length:

The min alignment length to be
select (bp), default: 10000

Min Alignment Length:

The min alignment identity to be
select (%), default: 90

Min Alignment Identity:

Plot a colinearity graph between draft genome
and reference genome. (will cost more time)

Plot:

RESET

GapFiller

Step1: Uploading gap closer sequence

Upload gap closer sequence:

Upload gap closer sequence

Gap closer sequence, allow multiple files (FASTA Format)

Step2: Setting algorithm parameters

Hover the mouse over the parameter label to see detailed description.
You may input values outside the range directly in the input box, but may not receive satisfactory result.

The min alignment length to be
select (bp), default: 1000

Min Alignment Length:

The min alignment identity to
be select (%), default: 40

Min Alignment Identity:

The flanking seq length of gap used
to anchor (bp), default: 5000

Flanking Sequence Length:

The max sequence length acceptable
to fill any gaps, default: 1000000

Max Filling Length:

RESET

TeloExplorer

Step1: Setting algorithm parameters

Hover the mouse over the parameter label to see detailed description.
You may input values outside the range directly in the input box, but may not receive satisfactory result.

The min repeat times to be
reported, default: 100

Min Repeat Times:

Specify clade of this genome.
Plant will search TTTAGGG,
animal will search TTAGGG,
other will use tidk explore's
suggestion default: other

Clade:

RESET

CentroMiner

Step1: Setting algorithm parameters

Hover the mouse over the parameter label to see detailed description.
You may input values outside the range directly in the input box, but may not receive satisfactory result.

Period (monomer length) range to be
consider as centromere repeat
monomer. Default: 100~200

Period:

—

Max allowed gap size between two
tandem repeats to be considered
as in one tandem repeat region.
Default: 50000

Max Gap:

Min size of tandem repeat region
to be selected as candidate.
Default: 100000

Min Length:

RESET

Submit Job

Please leave your email here. Once job is completed, we will send the Job ID to your email for retrieving results.
Click RUN button to submit your job.

RUN