Custom arguments

This page collects the tuning arguments that shape how EEfinder merges and filters elements, with worked examples.

Keeping temporary files

By default EEfinder archives its intermediate files under tmp_files/ inside the output directory. Pass -rm/--removetmp to delete them after a successful run instead.

Merging fragmented elements

Endogenous viruses are ancestral integrations, and the endogenised regions accumulate deletions and insertions over time. As a result a single ancestral integration can survive as several fragments with slightly different — or truncated — taxonomic assignments, so the current taxonomic levels may not reflect the classification of the ancestral virus. Two arguments let you merge such fragments.

Merge length (-lm / --limit)

Adjusts the distance used to merge two or more endogenous elements of the same taxon (as defined by --merge_level) and the same sense within a given range. A larger value merges neighbouring fragments that a stricter value would keep apart. It is passed straight to bedtools merge -d (default 1).

Merge level (-ml / --merge_level)

Selects the taxonomic level — genus (default) or family — used to decide whether two neighbouring elements belong to the “same taxon” for merging. Merging at family is more permissive: fragments assigned to different genera of one family are joined, which a genus-level merge keeps separate.

Elements whose level is unknown are never merged by taxon — they fall back to being keyed on their own subject accession, so an unclassified fragment is only ever merged with itself.

Range junction (-rj / --range_junction)

Sets the range used to clean redundant hits during the similarity analysis. The filter is applied to the BLAST/DIAMOND results, keyed on the query name, the start range of the query and the sense, so overlapping hits describing the same region collapse to the single best-scoring one (default 100).

Worked example — the three input hits all describe the same region, so EEfinder keeps only the best-scoring one and records its sense:

Input

qseqid	sseqid	pident	length	mismatch	gapopen	qstart	qend	sstart	send	evalue	bitscore
aag2_ctg_162	AAC97621	30.636	173	108	3	130612	130100	132	294	2.43e-08	69.7
aag2_ctg_162	AAU10897	23.611	216	163	2	130717	130073	134	348	2.52e-10	75.3
aag2_ctg_162	AOC55195	24.535	269	197	4	130864	130073	84	351	4.49e-11	77.8

Output

qseqid	sseqid	pident	length	mismatch	gapopen	qstart	qend	sstart	send	evalue	bitscore	sense
aag2_ctg_162	AOC55195	24.535	269	197	4	130073	130864	84	351	4.49e-11	77.8	neg

Both AAC97621 and AAU10897 cover the same region as AOC55195, so they are removed as redundant; the surviving hit’s coordinates are re-ordered ascending and its sense (neg) is recorded in a dedicated column.

Alignments shorter than 33 aa are discarded at the same step, regardless of --range_junction.

Minimum contig length (-ln / --length)

Sets the minimum length of contigs passed to BLAST/DIAMOND. Contigs shorter than this are dropped before the search (default 10000; lower it for short test contigs, as in the example run).

Flank length (-fl / --flank)

Sets the length of the flanking regions extracted around each endogenous element into PREFIX.EEs.flanks.fa (default 10000 nt on each side). The extraction uses bedtools slop, so flanks are clipped at contig boundaries rather than running past them.

Masking (-cm / --clean_masked and -mp / --mask_per)

Endogenous elements frequently sit inside repetitive regions, which many genome assemblies deliver soft-masked (lower-case). With -cm, EEfinder writes an additional, filtered pair of outputs (PREFIX.EEs.cleaned.fa and PREFIX.EEs.cleaned.tax.tsv) containing only the elements whose lower-case-plus-N content is at or below -mp percent (default 50).

The unfiltered PREFIX.EEs.fa / PREFIX.EEs.tax.tsv are always written too, so the flag adds a view rather than replacing one. Without -cm no masking filter is applied and -mp has no effect.

Output prefix (-pr / --prefix)

Names the prefix EEfinder uses for output files and element names. Sequence headers are formatted as PREFIX/CONTIG:START-END (e.g. Ae_aeg_Aag2_ctg_1913/ctg_1913:1754-2689); the taxonomy table’s Element-ID column carries the same name without the PREFIX/ part. We suggest combining the genome and assembly names, e.g. Ae_aeg_Aag2 for Aedes aegypti / Aag2.

If -pr is omitted the prefix is derived from the input filename, up to the first dot.