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Analyze

Overview

The analyze command predicts HGT-derived genes based on the distribution of the patterns of sequence homology search results of all proteins (genes) in one or more samples (genomes). Several statistical approaches are involved in this workflow.

hgtector analyze -i sample.tsv -o <output_dir> <parameters...>

The underlying procedures and the guideline for tuning parameters are explained in detail in second run.

Input

The input may be a file or a directory of files which are the output of the search command.

Output

File Description
scores.tsv A single multi-Fasta file containing all protein sequences.
hgts/<sample>.txt Predicted HGT-derived genes and their silhouette scores.
<group>.hist.png Histogram of scores of a group.
<group>.kde.png Density function of scores of a group, and clustering threshold (grey line).
scatter.png Scatter plot of distal vs. close scores. Each point represents a gene (protein).

Format of scores.tsv:

Field Description
sample Sample ID
protein Protein ID
length Protein length (aa)
hits Total number of hits after filtering
self, close, distal Score (sum of normalized bit scores) of each group
match Best match in "distal" group which implicates potential donor for predicted HGTs

Format of hgts/<sample>.txt:

Field Description
1 Protein ID
2 Silhouette score
3 Potential donor

Command-line reference

Basic

Option Default Description
-i, --input - Input search result file, or directory where one or more input files are located.
-o, --output - Directory where analysis results will be saved.
-t, --taxdump - Directory of taxonomy database files (nodes.dmp and names.dmp). Required if they are not found in input directory.

Hit filtering

Option Default Description
-k, --maxhits - Maximum number of sequence similarity search hits per gene (protein) to preserve.
--evalue - Maximum E-value cutoff.
--identity - Minimum percent identity cutoff.
--coverage - Minimum percent query coverage cutoff.

Taxonomic assignment

Option Default Description
--input-tax - TaxIDs of input samples. Will auto-infer if omitted. Can be comma-delimited, colon-inserted string (sample1:taxId1,sample2:taxId2...), or a file in the format of sample <tab> taxId.
--input-cov 75 For auto-inference: an input sample will be assigned to a taxon if it represents this percentage or more best hits.

Taxonomic grouping

Option Default Description
--self-tax - TaxIDs of "self" group (a comma-delimited string, or a file of one TaxID per line). Will auto-infer if omitted.
--close-tax - TaxIDs of "close" group (a comma-delimited string, or a file of one TaxID per line). Will auto-infer if omitted.
--self-rank - For auto-inference: "self" group must be at or above this rank (e.g., species, genus, family...).
--close-size 10 For auto-inference: "close" group must have at least this number of taxa.

Scoring

Option Default Description
--weighted yes Score is sum of weighted bit scores; otherwise simple counts.

Filtering

Option Default Description
--outliers zscore Detect and remove outliers using selected method (none, zscore, boxplot).
--orphans no Keep orphans (proteins without non-self hits) in statistical analysis.

Prediction

Option Default Description
--bandwidth auto Bandwidth for Gaussian KDE (auto, grid, silverman, or a number between 0.1 and 1.0).
--bw-steps 20 Number of steps for auto and grid kernel bandwidth optimization.
--low-part 75 Maximum percentage below threshold for automatic bandwidth optimization.
--noise 50 Percent valley-to-peak distance to exclude from cluster.
--fixed 25 Use this percentage as threshold if KDE clustering fails.
--silhouette 0.5 Silhouette score threshold for cluster refinement.
--self-low no HGT has low "self" score (an optional criterion).

Donor reporting

Option Default Description
--distal-top 10 Find a match in "distal" group which is LCA of hits with bit score at most this percentage lower than the best hit. The behavior is consistent with DIAMOND's --top parameter. This match implicates the potential donor of an HGT-derived gene.
--donor-name - Report taxon name instead of TaxID of donor.
--donor-rank - Report donor at this rank (e.g., genus, family...). A donor below this rank will be raise to this rank; a donor above this rank will be discarded. If unspecified, the donor will be the LCA of top hits from the distal group.

Program behavior

Option Default Description
--from-scores - If a score table already exists, use it and skip search result parsing and taxonomy inference. Otherwise overwrite it.