Glossary of tags

Fri, 04 Oct 2024 17:16:03 +0200

Glossary of tags #

A #

ac: Accession number of the ecoPCR record used as template. ( obiconvert)
aho_corasick: Total number of occurrences of the provided motifs detected by the Aho–Corasick search. ( obiannotate)
aho_corasick_Fwd: Number of motif matches on the forward strand when running the Aho–Corasick scanner. ( obiannotate)
aho_corasick_Rev: Number of motif matches on the reverse complement strand produced by the Aho–Corasick scanner. ( obiannotate)
ali_dir: Orientation of the alignment window when overlapping reads are aligned ("left" or "right"). ( obikmersim, obipairing)
ali_length: Length of the aligned region considered when assembling paired reads. ( obikmersim, obipairing)
amplicon_length: Expected size of the in silico amplicon described in an ecoPCR record. ( obiconvert)

C #

chimera: Flag produced by obiclean identifying sequences detected as chimeric. ( obiclean)
count: Number of occurrences of the dereplicated sequence in the dataset.

D #

definition: Text description kept from the original FASTA/FASTQ definition line.
demultiplex_error: Human‑readable reason explaining why a read could not be assigned to a PCR sample. ( obimultiplex, obipcr)
direction: Orientation of the read with respect to the primer set (forward or reverse). ( obimultiplex, obipcr)

E #

experiment: Experiment identifier assigned to each multiplexed sample in the NGS filter. ( obimultiplex, obitagpcr)

F #

family_name: Scientific name of the family containing the ecoPCR reference sequence. ( obiconvert)
family_taxid: NCBI taxid of the family containing the ecoPCR reference sequence. ( obiconvert)
forward_error: Number of mismatches tolerated between the read and the forward primer. ( obimultiplex, obipcr)
forward_match: Sequence of the forward primer match extracted from the read. ( obimultiplex, obipcr)
forward_mismatch: Mismatch count reported in ecoPCR reference entries for the forward primer. ( obiconvert)
forward_primer: Forward primer sequence used while demultiplexing or during in silico PCR. ( obiconvert, obimultiplex, obipcr)
forward_tag: Sample tag (index) identified on the forward side of a read. ( obimultiplex, obipcr)
forward_tm: Melting temperature of the forward primer reported by ecoPCR. ( obiconvert)

G #

genus_name: Scientific name of the genus containing the ecoPCR reference sequence. ( obiconvert)
genus_taxid: NCBI taxid of the genus containing the ecoPCR reference sequence. ( obiconvert)

L #

landmark_coord: Coordinate of a reference sequence in the landmark space produced by obilandmark. ( obilandmark)
landmark_id: Identifier of the landmark sequence used as axis when building the landmark space. ( obilandmark)

M #

merged_sample: Map storing the abundance of each sample contributing to a merged record. ( obimatrix, obiuniq)
microsat: Sequence of the detected microsatellite region. ( obimicrosat)
microsat_from: 1-based start position of the detected microsatellite. ( obimicrosat)
microsat_left: Left flanking region kept around the detected microsatellite. ( obimicrosat)
microsat_right: Right flanking region kept around the detected microsatellite. ( obimicrosat)
microsat_to: End position (1-based, inclusive) of the detected microsatellite. ( obimicrosat)
microsat_unit: Minimal repeat unit sequence describing the microsatellite. ( obimicrosat)
microsat_unit_count: Number of times the minimal unit is repeated inside the microsatellite. ( obimicrosat)
microsat_unit_length: Length (in bases) of the minimal repeat unit in the microsatellite. ( obimicrosat)
microsat_unit_normalized: Canonical representation of the repeat unit, normalized for strand orientation. ( obimicrosat)
microsat_unit_orientation: Orientation ("direct" or "reverse") of the repeat unit with respect to the original read. ( obimicrosat)
mode: Whether a paired-read assembly comes from an actual alignment or from simply joining reads. ( obipairing)

O #

obiclean_cluster: Identifier of the obiclean cluster containing the sequence. ( obiclean)
obiclean_head: Boolean flag indicating that the sequence is the most abundant variant in its cluster. ( obiclean)
obiclean_headcount: Abundance of the cluster head sequence. ( obiclean)
obiclean_internalcount: Cumulated abundance of internal (non-head, non-singleton) variants in the obiclean cluster. ( obiclean)
obiclean_mutation: Edit description used by obiclean to label the relationship between a sequence and its head. ( obiclean)
obiclean_samplecount: Total abundance (head + internal + singleton) of the obiclean cluster. ( obiclean)
obiclean_singletoncount: Number of singleton variants linked to the head in the obiclean graph. ( obiclean)
obiclean_status: Final obiclean status (head/internal/singleton/bad) attributed to the sequence. ( obiclean)
obiclean_weight: Relative weight computed for each sequence during obiclean consensus building. ( obiclean)
obicleandb_dist: Distance distribution between a reference and its neighbors during database cleaning. ( obicleandb)
obicleandb_level: Taxonomic rank (none/genus/family) reached during the obicleandb validation workflow. ( obicleandb)
obicleandb_median: Median similarity score within the accepted cluster around a reference sequence. ( obicleandb)
obicleandb_scores: Raw similarity scores observed for the reference during database validation. ( obicleandb)
obicleandb_trusted: Probability assigned by obicleandb that the reference sequence is trustworthy. ( obicleandb)
obicleandb_trusted_on: Number of supporting sequences used to compute the obicleandb trust score. ( obicleandb)
obiconsensus_consensus: Boolean flag indicating whether a sequence is a consensus sequence produced by obiconsensus. ( obiconsensus)
obiconsensus_filtered_graph_size: Size of the kmer graph after filtering low-coverage nodes. ( obiconsensus)
obiconsensus_full_graph_size: Size of the full kmer graph before filtering. ( obiconsensus)
obiconsensus_kmer_max_occur: Maximum abundance observed for any kmer in the graph used to build the consensus. ( obiconsensus)
obiconsensus_kmer_size: Kmer size actually used to build the consensus for the sequence. ( obiconsensus)
obiconsensus_seq_length: Length of the consensus sequence returned by obiconsensus. ( obiconsensus)
obiconsensus_weight: Cumulated weight (number of supporting reads) of the consensus sequence. ( obiconsensus)
obikmer_ali_length: Alignment length between the query and the best kmer-matched reference. ( obikmersim)
obikmer_fast_count: Number of shared kmers discovered during the fast filtering phase. ( obikmersim)
obikmer_fast_overlap: Estimated overlap length inferred from the kmer matching step. ( obikmersim)
obikmer_fast_score: Fast alignment score computed before the full alignment stage. ( obikmersim)
obikmer_identity: Proportion of identical bases in the alignment computed after kmer matching. ( obikmersim)
obikmer_kmer_size: Size of the kmers that were indexed to perform the similarity search. ( obikmersim)
obikmer_match_count: Number of references sharing at least the requested number of kmers with the query. ( obikmersim)
obikmer_match_id: Identifier of the reference sequence selected as best match for a query ("-rev" when aligning the reverse complement). ( obikmersim)
obikmer_orientation: Orientation (forward/reverse) used when aligning the query to the best kmer match. ( obikmersim)
obikmer_residual_id: Identity computed after removing the minimal number of shared kmers from the alignment. ( obikmersim)
obikmer_score: Alignment score resulting from the Smith–Waterman extension after kmer matching. ( obikmersim)
obikmer_score_norm: Alignment score normalized by alignment length for kmer-based matches. ( obikmersim)
obikmer_sparse_kmer: Indicates whether sparse kmers were used while building the index. ( obikmersim)
obimultiplex_amplicon_rank: Rank of the barcode match among all amplicons compatible with the read. ( obimultiplex)
obimultiplex_direction: Orientation of the read determined during barcode extraction (forward or reverse). ( obimultiplex, obitagpcr)
obimultiplex_error: Explanation of the failure encountered during barcode extraction. ( obimultiplex, obitagpcr)
obimultiplex_forward_error: Mismatch count observed between the read and the forward primer in the NGS filter. ( obimultiplex, obitagpcr)
obimultiplex_forward_match: Portion of the read matching the forward primer. ( obimultiplex, obitagpcr)
obimultiplex_forward_matching: Matching model (strict/hamming/indel) used to interpret the forward primer. ( obimultiplex)
obimultiplex_forward_mismatches: Forward primer mismatch count propagated to paired reads during PCR tagging. ( obitagpcr)
obimultiplex_forward_primer: Forward primer sequence fetched from the NGS filter entry assigned to the read. ( obimultiplex)
obimultiplex_forward_proposed_tag: Forward tag proposed by the error-tolerant search before validation. ( obimultiplex)
obimultiplex_forward_tag: Forward sample tag assigned to the read. ( obimultiplex, obitagpcr)
obimultiplex_forward_tag_dist: Edit distance between the observed tag and the expected forward tag. ( obimultiplex)
obimultiplex_reverse_error: Mismatch count observed between the read and the reverse primer in the NGS filter. ( obimultiplex, obitagpcr)
obimultiplex_reverse_match: Portion of the read matching the reverse primer. ( obimultiplex, obitagpcr)
obimultiplex_reverse_matching: Matching model (strict/hamming/indel) used to interpret the reverse primer. ( obimultiplex)
obimultiplex_reverse_mismatches: Reverse primer mismatch count propagated to paired reads during PCR tagging. ( obitagpcr)
obimultiplex_reverse_primer: Reverse primer sequence fetched from the NGS filter entry assigned to the read. ( obimultiplex)
obimultiplex_reverse_proposed_tag: Reverse tag proposed by the error-tolerant search before validation. ( obimultiplex)
obimultiplex_reverse_tag: Reverse sample tag assigned to the read. ( obimultiplex, obitagpcr)
obimultiplex_reverse_tag_dist: Edit distance between the observed tag and the expected reverse tag. ( obimultiplex)
obisplit_frg: Index of the fragment produced by obisplit from the original read. ( obisplit)
obisplit_group: Name of the splitting group (pool or pattern pair) to which the fragment belongs. ( obisplit)
obisplit_left_error: Mismatch count tolerated on the left delimiting pattern. ( obisplit)
obisplit_left_match: Sequence matched by the left delimiting pattern. ( obisplit)
obisplit_left_pattern: Name of the pattern that delimited the left boundary. ( obisplit)
obisplit_location: Coordinates of the fragment extracted by obisplit (start..end, 1-based). ( obisplit)
obisplit_nfrg: Total number of fragments produced from the source read. ( obisplit)
obisplit_right_error: Mismatch count tolerated on the right delimiting pattern. ( obisplit)
obisplit_right_match: Sequence matched by the right delimiting pattern. ( obisplit)
obisplit_right_pattern: Name of the pattern that delimited the right boundary. ( obisplit)
obisplit_set: Label of the pattern set (pool) used to extract a fragment. ( obisplit)
obitag_bestid: Best identity score obtained when tagging a sequence with reference databases. ( obitag)
obitag_bestmatch: Identifier of the best matching reference sequence used for taxonomic assignment. ( obitag)
obitag_coord: Geographic coordinates of the query when using geometric tagging. ( obitag)
obitag_geomref_index: Distance index (difference → taxon) stored for landmark-based geometric tagging. ( obirefidx, obitag)
obitag_match_count: Number of reference sequences sharing the best score with the query. ( obitag)
obitag_min_dist: Minimal geometric distance observed between the query and landmark references. ( obitag)
obitag_rank: Taxonomic rank associated with the assigned reference taxon. ( obitag)
obitag_ref_index: Precomputed index linking mismatch counts to reference taxa for LCS-based tagging. ( obirefidx, obitag)
obitag_similarity_method: Identification method used by obitag ("lcs" or "geometric"). ( obitag)

P #

pair:
pairing_fast_count: Number of kmers supporting the initial overlap detection between paired reads. ( obipairing)
pairing_fast_overlap: Expected overlap length estimated from the fast pre-alignment step. ( obipairing)
pairing_fast_score: Score computed during the fast overlap detection stage prior to full alignment. ( obipairing)
pairing_mismatches: Map describing positions and base substitutions observed when merging paired reads. ( obipairing)
pattern: Pattern sequence tested with obiannotate --pattern; the tag name is prefixed when --pattern-name is provided. ( obiannotate)
pattern_error: Number of mismatches or indels between the queried pattern and the matched subsequence (prefix follows pattern name). ( obiannotate)
pattern_location: Genomic coordinates (forward or complement) of the matched pattern (prefix follows pattern name). ( obiannotate)
pattern_match: Sequence fragment that matched the requested pattern (prefix follows pattern name). ( obiannotate)

R #

rank: Taxonomic rank assigned to the ecoPCR reference sequence. ( obiconvert)
reffamidx_cluster_n: Number of clusters created when indexing a family-level reference database. ( obirefidx)
reffamidx_clusterhead: Boolean flag telling whether the reference sequence is the head of its similarity cluster. ( obirefidx)
reffamidx_clusterid: Identifier of the cluster head that represents a reference sequence. ( obirefidx)
reffamidx_clusteridentity: Pairwise identity between a reference sequence and the head of its family cluster. ( obirefidx)
reffamidx_id: Unique identifier assigned to each reference sequence while building the family index. ( obirefidx)
reffamidx_in: Index structure created for a given reference sequence to accelerate taxonomic assignment. ( obirefidx)
reverse_error: Number of mismatches tolerated between the read and the reverse primer. ( obimultiplex, obipcr)
reverse_match: Sequence of the reverse primer match extracted from the read. ( obimultiplex, obipcr)
reverse_mismatch: Mismatch count reported in ecoPCR reference entries for the reverse primer. ( obiconvert)
reverse_primer: Reverse primer sequence used while demultiplexing or during in silico PCR. ( obiconvert, obimultiplex, obipcr)
reverse_tag: Sample tag identified on the reverse side of a read. ( obimultiplex, obipcr)
reverse_tm: Melting temperature of the reverse primer reported by ecoPCR. ( obiconvert)

S #

sample: Sample identifier assigned by the NGS filter and propagated to annotated reads. ( obimultiplex, obitagpcr)
scientific_name: Scientific name for the current taxonomic annotation. ( obiannotate, obiconvert, obitag)
score: Alignment score computed while merging paired reads. ( obipairing)
score_norm: Alignment score normalized by the overlap length when assembling paired reads. ( obikmersim, obipairing)
seq_a_single: Number of nucleotides trimmed from sequence A because they are single-stranded in the overlap. ( obikmersim, obipairing)
seq_ab_match: Number of matching positions observed in the aligned overlap between two sequences. ( obikmersim, obipairing)
seq_b_single: Number of nucleotides trimmed from sequence B because they are single-stranded in the overlap. ( obikmersim, obipairing)
seq_length: Length of the sequence in nucleotides. ( obiannotate, obikmersim, obimicrosat)
seq_number: Ordinal number assigned to sequences when numbering is requested or needed for taxonomy extraction. ( obiannotate, obiconvert)
species_name: Scientific name of the species associated with the ecoPCR reference sequence. ( obiconvert)
species_taxid: NCBI taxid of the species associated with the ecoPCR reference sequence. ( obiconvert)
strand: Strand orientation stored in the ecoPCR record. ( obiconvert)

T #

taxid: Taxonomic identifier of the sequence within the current taxonomy. ( obiconvert, obipcr, obitag)
taxonomic_path: Ordered list of taxids describing the lineage of the annotated sequence. ( obiannotate)
taxonomic_rank: Rank name corresponding to the assigned taxon. ( obiannotate)

The OBITools4 commands on OBITools4 documentation

Glossary of tags

Glossary of tags #

A #

C #

D #

E #

F #

G #

L #

M #

O #

P #

R #

S #

T #