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OBICLEAN(1) OBITools OBICLEAN(1)

NAME

obiclean - description of obiclean

obiclean is a command that classifies sequence records either as head, internal or singleton.

  • sequence record counts
  • sequence similarities

  • count of S1 divided by count of S2 is lesser than the ratio R. R default value is set to 1, and can be adjusted between 0 and 1 with the -r option.
  • both sequences are related to one another (they can align with some differences, the maximum number of differences can be specified by the -d option).

•
  • there exists at least one sequence record in the dataset that is a variant of S
  • there exists no sequence record in the dataset such that S is a variant of this sequence record


•
•
there exists at least one sequence record in the dataset such that S is a variant of this sequence record


•
  • there exists no sequence record in the dataset that is a variant of S
  • there exists no sequence record in the dataset such that S is a variant of this sequence record




By default, tagging is done once for the whole dataset, but it can also be done sample by sample by specifying the -s option. In such a case, the counts are extracted from the sample information.

Finally, each sequence record is annotated with three new attributes head, internal and singleton. The attribute values are the numbers of samples in which the sequence record has been classified in this manner.

OBICLEAN SPECIFIC OPTIONS

Maximum numbers of differences between two variant sequences (default: 1).

Attribute containing sample descriptions.

Threshold ratio between counts (rare/abundant counts) of two sequence records so that the less abundant one is a variant of the more abundant (default: 1, i.e. all less abundant sequences are variants).

Switch obiclean into its clustering mode. This adds information to each sequence about the true.

Select only sequences with the head status in a least one sample.

Creates a file containing the set of DAG used by the obiclean clustering algorithm. The graph file follows the dot format

OPTIONS TO SPECIFY INPUT FORMAT

Restrict the analysis to a sub-part of the input file

The N first sequence records of the file are discarded from the analysis and not reported to the output file

Only the N next sequence records of the file are analyzed. The following sequences in the file are neither analyzed, neither reported to the output file. This option can be used conjointly with the –skip option.

Sequence annotated format

Input file is in genbank format.

Input file is in embl format.

Input file is in fasta format (including OBITools fasta extensions).

Input file is in Sanger fastq format (standard fastq used by HiSeq/MiSeq sequencers).

Input file is in fastq format produced by Solexa (Ga IIx) sequencers.

Input file is in ecoPCR format.

Input is an ecoPCR database.

Specifying the sequence type

Input file contains nucleic sequences.

Input file contains protein sequences.

OPTIONS TO SPECIFY OUTPUT FORMAT

Standard output format

--fasta-output
Output sequences in OBITools fasta format

Output sequences in Sanger fastq format

Generating an ecoPCR database

--ecopcrdb-output=<PREFIX_FILENAME>
Creates an ecoPCR database from sequence records results

Miscellaneous option

Print sequences in upper case (default is lower case)

COMMON OPTIONS

Shows this help message and exits.

Sets logging in debug mode.

OBICLEAN USED SEQUENCE ATTRIBUTES

•
count






OBICLEAN ADDED SEQUENCE ATTRIBUTES

  • obiclean_cluster
  • obiclean_count
  • obiclean_head

  • obiclean_headcount
  • obiclean_internalcount
  • obiclean_samplecount

  • obiclean_singletoncount
  • obiclean_status




AUTHOR

The OBITools Development Team - LECA

COPYRIGHT

2019 - 2015, OBITool Development Team

January 28, 2019 1.02 12