PolishTE is a simple bash pipeline for extension and edge polishing of transposable elements consensi. The extension of TE ends step can be important, even essential, for genotyping and identifying new insertions on new genomes.
The program take as input a putative TE sequence and the reference genome used for the annotation and it returns the polished sequence.
More in details, the program starts with a blastn against the genome, if several hits come from the same fragment on the genome the sequence is marked as simple repeat, otherwise a random sampling of hits is done (by default it samples 100 hits where 25 are the longer ones).
Then, sequences corresponding to hits are extracted from the genome with a flanking region (by default 1000bp for each end) using bedtool slop. These sequences are aligned with mafft and then the MSA is cleaned using CIAlign and a new consensus is called.
If this one is close to the original sequence it means that sequence can't extend and the new sequence is returned. In contrast, if it is sufficiently different, it means that the consensus can still expand or shorten. So, a check for the ends coverage is done, if they are high covered it means that sequence can still extend and more flanking bases are added. Otherwise, if they are low covered (or not covered at all) it means that the sequences has been far too extended and the sequence need to be trimmed.
After that, the extended/trimmed sequence is used in a new cycle blastn-mafft-CIAlign and the new consensus is compared with that of the previous iteration. The program loop until the consensus stop to be update or a time limit is reached.
mafft(tested version: v7.490 (2021/Oct/30))blastn(tested version: 2.9.0+)samtools(tested version: 1.10)awk(tested version: 5.0.1)bedtools(tested version: v2.27.1)CIAlign(tested version: 1.0.15)python3(tested version: 3.10.2)python-Levenshtein(tested version: 0.12.2)
R(tested version: 3.6.3)
git clone https://github.com/TommasoBarberis/polishTE.git
chmod +x polishTE
singularity pull library://tommasobarberis98/tealb/polishte
polishTE -i seq.fasta -g ref.fasta [OPTIONS]
singularity exec polishTE.sif polishTE -i seq.fasta -g ref.fasta
| Parameter | Description | Default |
|---|---|---|
-i, --input |
FASTA file with the sequence to polish | None |
-g, --genome |
FASTA file with the reference | None |
-h, --help |
show the help message | None |
-t, --threads |
number of threads to use in the multiple alignement with MAFFT |
1 |
-o, --output |
output directory | ./ |
-min, --min_length |
Minmum length for blastn hits that will be recovered in the genome. If the option is set to 0, the program will use the half of the length of the TE as minimum length, else it will use the provided value |
0 |
-f, --flank |
Number of bases to extract at the flanking regions (5' and 3') of the hits | 1000pb |
-e, --evalue |
e-value threshold for the blastn |
1e-20 |
-l, --limit |
Maximum number of hits to take in account for the alignment. If the number of hits is less then this limit, the subsample is skipped. | 100 |
-k, --keep_longest |
Keep the <k> % longest sequences among the blastn hits |
0.25 |
-ins, --max_ins_size |
Remove an insertion from the MSA if its size is less than <ins> (range:[200-1000]) | 200 |
-m, --mode |
Speed mode. fast and less accurate (max 10 iterations) or slow and more accurate (max 100 iterations). When the maximum number of iteration is reached, the program is interrupted and it returns any sequence | fast |
-c, --min_cov |
Minimum coverage on boundaries to perform the extension | 3 |
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