Bioinformatics at COMAV

clean_reads

Warning: We consider clean_reads an obsolete project. We are now focusing our efforts in our tool set, seq_crumbs. Not all functionalities of clean_reads have been implemented in seq_crumbs yet, but most are working. If you need anything not yet implemented, please let us know.

clean_reads cleans NGS (Sanger, 454, Illumina and solid) reads. It can trim:

  • bad quality regions,
  • adaptors,
  • vectors, and
  • regular expresssions.

It also filters out the reads that do not meet a minimum quality criteria based on the sequence length and the mean quality.

It uses several algorithms and third party tools to carry out the cleaning. The third party tools used are: lucy, blast, mdust and trimpoly.

The functionality offered by clean_reads is similar to the cleaning capabilities of the ngs_backbone pipeline. In fact, both tools use the same code base and are just different interfaces on top of a Python library called franklin.

Help

To get help you can use the ngs_backbone maling list. If you have any question send an email to the list: ngs_backbone@upv.es

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