q2-fragment-insertion

No description available. See plugin website: https://github.com/qiime2/q2-fragment-insertion

version: 2024.10.0

website: https://github.com/qiime2/q2-fragment-insertion

user support:

https://github.com/qiime2/q2-fragment-insertion/issues

citations:

Janssen et al., 2018; Matsen et al., 2012; Eddy, 2011; Matsen et al., 2010

Actions¶

Artifact Classes¶

Formats¶

fragment-insertion sepp¶

Perform fragment insertion of sequences using the SEPP algorithm.

Citations¶

Janssen et al., 2018; Matsen et al., 2012; Eddy, 2011; Matsen et al., 2010

Inputs¶

representative_sequences: FeatureData[Sequence]

The sequences to insert into the reference tree.[required]

reference_database: SeppReferenceDatabase

The reference database to insert the representative sequences into.[required]

Parameters¶

alignment_subset_size: Int

Each placement subset is further broken into subsets of at most these many sequences and a separate HMM is trained on each subset.[default: 1000]

placement_subset_size: Int

The tree is divided into subsets such that each subset includes at most these many subsets. The placement step places the fragment on only one subset, determined based on alignment scores. Further reading: tutorial/sepp-tutorial.md.[default: 5000]

threads: Threads

The number of threads to use. Pass 0 to use one per available core.[default: 1]

debug: Bool

Collect additional run information to STDOUT for debugging. Temporary directories will not be removed if run fails.[default: False]

Outputs¶

tree: Phylogeny[Rooted]

The tree with inserted feature data.[required]

placements: Placements

Information about the feature placements within the reference tree.[required]

fragment-insertion classify-otus-experimental¶

Experimental: Use the resulting tree from 'sepp' and find closest OTU-ID for every inserted fragment. Then, look up the reference lineage string in the reference taxonomy.

Citations¶

Janssen et al., 2018; Matsen et al., 2012; Eddy, 2011; Matsen et al., 2010

Inputs¶

representative_sequences: FeatureData[Sequence]

The sequences used for a 'sepp' run to produce the 'tree'.[required]

tree: Phylogeny[Rooted]

The tree resulting from inserting fragments into a reference phylogeny, i.e. the output of function 'sepp'[required]

reference_taxonomy: FeatureData[Taxonomy]

Reference taxonomic table that maps every OTU-ID into a taxonomic lineage string.[required]

Outputs¶

classification: FeatureData[Taxonomy]

Taxonomic lineages for inserted fragments.[required]

fragment-insertion filter-features¶

Filters fragments not inserted into a phylogenetic tree from a feature-table. Some fragments computed by e.g. Deblur or DADA2 are too remote to get inserted by SEPP into a reference phylogeny. To be able to use the feature-table for downstream analyses like computing Faith's PD or UniFrac, the feature-table must be cleared of fragments that are not part of the phylogenetic tree, because their path length can otherwise not be determined. Typically, the number of rejected fragments is low (<= 10), but it might be worth to inspect the ratio of reads assigned to those rejected fragments.

Citations¶

Janssen et al., 2018; Matsen et al., 2012; Eddy, 2011; Matsen et al., 2010

Inputs¶

table: FeatureTable[Frequency]

A feature-table which needs to filtered down to those fragments that are contained in the tree, e.g. result of a Deblur or DADA2 run.[required]

tree: Phylogeny[Rooted]

The tree resulting from inserting fragments into a reference phylogeny, i.e. the output of function 'sepp'[required]

Outputs¶

filtered_table: FeatureTable[Frequency]

The input table minus those fragments that were not part of the tree. This feature-table can be used for downstream analyses like phylogenetic alpha- or beta- diversity computation.[required]

removed_table: FeatureTable[Frequency]

Those fragments that got removed from the input table, because they were not part of the tree. This table is mainly used for quality control, e.g. to inspect the ratio of removed reads per sample from the input table. You can ignore this table for downstream analyses.[required]