Appendix A — Annexes

A.1 Sequence attributes

ali_dir (string)

Set by the obipairing tool
The attribute can contain 2 string values left or right.

The alignment generated by obipairing is a 3’-end gap free algorithm. Two cases can occur when aligning the forward and reverse reads. If the barcode is long enough, both the reads overlap only on their 3’ ends. In such case, the alignment direction ali_dir is set to left. If the barcode is shorter than the read length, the paired reads overlap by their 5’ ends, and the complete barcode is sequenced by both the reads. In that later case, ali_dir is set to right.

ali_length (int)

Set by the obipairing tool

Length of the aligned parts when merging forward and reverse reads

count (int)

Set by the obiuniq tool
Getter : method Count()
Setter : method SetCount(int)

The count attribute indicates how-many strictly identical reads have been merged in a single record. It contains an integer value. If it is absent this means that the sequence record represents a single occurrence of the sequence.

The Count() method allows to access to the count attribute as an integer value. If the count attribute is not defined for the given sequence, the value 1 is returned

merged_* (map[string]int)

Set by the obiuniq tool

The -m option of the obiuniq tools allows for keeping track of the distribution of the values stored in given attribute of interest. Often this option is used to summarise distribution of a sequence variant accross samples when obiuniq is run after running obimultiplex. The actual name of the attribute depends on the name of the monitored attribute. If -m option is used with the attribute sample, then this attribute names merged_sample.

mode (string)

Set by the obipairing tool
The attribute can contain 2 string values join or alignment.

obitag_ref_index (map[string]string)

Set by the obirefidx tool.

It resumes to which taxonomic annotation a match to that sequence must lead according to the number of differences existing between the query sequence and the reference sequence having that tag.

   {"0":"9606@Homo sapiens@species",
    "2":"207598@Homininae@subfamily",
    "3":"9604@Hominidae@family",
    "8":"314295@Hominoidea@superfamily",
    "10":"9526@Catarrhini@parvorder",
    "12":"1437010@Boreoeutheria@clade",
    "16":"9347@Eutheria@clade",
    "17":"40674@Mammalia@class",
    "22":"117571@Euteleostomi@clade",
    "25":"7776@Gnathostomata@clade",
    "29":"33213@Bilateria@clade",
    "30":"6072@Eumetazoa@clade"}

pairing_mismatches (map[string]string)

Set by the obipairing tool

seq_a_single (int)

Set by the obipairing tool

seq_ab_match (int)

Set by the obipairing tool

seq_b_single (int)

Set by the obipairing tool

score (int)

Set by the obipairing tool

score_norm (float)

Set by the obipairing tool
The value ranges between 0 and 1.

Score of the alignment between forward and reverse reads expressed as a fraction of identity.