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Launch map analysis

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Can be gzipped. Must end with .fa, .fasta, .fna, .fa.gz, .fasta.gz or .fna.gz
Can be gzipped. Must end with .fa, .fasta, .fna, .fa.gz, .fasta.gz or .fna.gz
Repeatedness 
For large genomes keep the "Repeatedness" parameter set to "Many repeats". If not your job may be killed because of time limit or memory limit crossing.

This instance configuration

  • Uploaded file size is limited to 1.5 GiB.
  • When uncompressed, the size of each file is limited to:
    • 3.4 GiB in all vs all mode.
    • 3.9 GiB else.
  • Computation wall times are set to (hh:mm:ss):
    • 02:00:00 for preparation step,
    • 02:00:00 for align step.
In PAF or MAF format. Must end with .paf or .maf
Fasta file or index built by our tool. Must end with .fa, .fasta, .fna, .fa.gz, .fasta.gz, .fna.gz or .idx.
Fasta file or index built by our tool. Must end with .fa, .fasta, .fna, .fa.gz, .fasta.gz, .fna.gz or .idx.

- or -

TAR file from a previous run or built following this documentation. Must ends with .tar or .tar.gz

This instance configuration

  • Uploaded file size is limited to 1.5 GiB.
  • When uncompressed, the size of each file must be under 3.9 GiB
  • Computation wall time for indexing is set to 02:00:00 (hh:mm:ss).
Text file following batch format. Must end with .txt
File Size State Actions

Minimap2 v2.28

Better for low similar fasta files
Please use tool=minimap2

Options1

Default options are displayed in bold.
Please use options=key1,key2,... where keys are:

Repeatedness (mutually exclusive)

Trade-off between alignment precision and computation requirements (CPU Time + RAM) by ignoring the top fraction of most frequent minimizers

  • repeat:few : few repeats 
  • repeat:some : some repeats 
  • repeat:many : many repeats 

Mashmap v2.0

Faster for high similar fasta files
Please use tool=mashmap

Options1

No option.

1 Look at the batch format page for full description. Default options are displayed in bold