Tinscan: TE-Insertion-Scanner
Scan whole genome alignments for transposon insertion signatures.
Table of contents
Algorithm overview
- Perform gapped and chained whole genome alignment of query genome B onto target genome A.
- Where two aligned segments are contiguous in B (or separated by no more than --qGap), and
- Separated by an insertion in the range --minInsert:--maxInsert in A, and
- At least one flanking alignment in A satisfies the threshold --minIdent, and differs from its mate by no more than --maxIdentDiff %
- Log flanks and candidate insertion.
- Attempt to infer TSDs from the internal overlap of flanking alignments in B genome.
Options and usage
Installing Tinscan
Requirements:
- LASTZ genome alignment tool from the Miller Lab, Penn State.
Install from PyPi:
pip install tinscan
Clone and install from this repository:
git clone https://github.com/Adamtaranto/TE-insertion-scanner.git && cd TE-insertion-scanner && pip install -e .
Example usage
Find insertion events in genome A (target) relative to genome B (query).
Prepare Input Genomes
Split A and B genomes into two directories containing one scaffold per file. Check that sequence names are unique within genomes.
tinscan-prep --adir data/A_target_split --bdir data/B_query_split\
-A data/A_target_genome.fasta -B data/B_query_genome.fasta
Output: data/A_target_split/.fa data/B_query_split/.fa
Align Genomes
Align each scaffold from genome B onto each genome A scaffold. Report alignments with >= 60% identity and length >= 100bp.
tinscan-align --adir data/A_target_split --bdir data/B_query_split \
--outdir A_Inserts --outfile A_Inserts_vs_B.tab \
--minIdt 60 --minLen 100 --hspthresh 3000
Output: A_Inserts/A_Inserts_vs_B.tab
Note: Alignment tasks can be limited to a specified set of pairwise comparisons where appropriate (i.e. when homologous chromosome pairs are known between assemblies) using the option "--pairs". Comparisons are specified with a tab-delimited text file, where column 1 contains sequence names from genome A, and column 2 contains sequences from genome B.
In the example Chromosome_pairs.txt, Chr A2 has been assembled as two scaffolds (B2, B3) in genome B.
#Chromosome_pairs.txt
A1 B1
A2 B2
A2 B3
A3 B4
Find Insertions
Scan alignments for insertion events and report as GFF annotation of Genome A
tinscan-find --infile A_Inserts/A_Inserts_vs_B.tab \
--outdir A_Inserts --gffOut A_Inserts_vs_B_l100_id80.gff3 \
--maxInsert 50000 --minIdent 80 --maxIdentDiff 20
Output: A_Inserts/A_Inserts_vs_B_l100_id80.gff3
Standard options
tinscan-prep
tinscan-prep --help
Usage: tinscan-prep [-h] -A TARGET -B QUERY [--adir ADIR] [--bdir BDIR]
[-d OUTDIR]
Split multifasta genome files into directories for A and B genomes.
Optional arguments:
-h, --help Show this help message and exit.
-A , --target Multifasta containing A genome.
-B , --query Multifasta containing B genome.
--adir A genome sub-directory within outdir
--bdir B genome sub-directory within outdir
-d , --outdir Write split directories within this directory.
(Default: cwd)
tinscan-align
tinscan-align --help
Usage: tinscan-align [-h] --adir ADIR --bdir BDIR [--pairs PAIRS] [-d OUTDIR]
[--outfile OUTFILE] [--verbose] [--lzpath LZPATH]
[--minIdt MINIDT] [--minLen MINLEN]
[--hspthresh HSPTHRESH]
Align B genome (query) sequences onto A genome (target) using LASTZ.
Optional arguments:
-h, --help Show this help message and exit
--adir Name of the directory containing sequences from A genome.
--bdir Name of the directory containing sequences from B genome.
--pairs Optional: Tab-delimited 2-col file specifying
target:query sequence pairs to be aligned
-d , --outdir Write output files to this directory. (Default: cwd)
--outfile Name of alignment result file.
--verbose If set report LASTZ progress.
--lzpath Custom path to LASTZ executable if not in $PATH.
--minIdt Minimum alignment identity to report.
--minLen Minimum alignment length to report.
--hspthresh LASTZ min HSP threshold. Increase for stricter matches.
tinscan-find
tinscan-find --help
Usage: tinscan-find [-h] -i INFILE [--outdir OUTDIR] [--gffOut GFFOUT]
[--noflanks] [--maxTSD MAXTSD] [--maxInsert MAXINSERT]
[--minInsert MININSERT] [--qGap QGAP]
[--minIdent MINIDENT] [--maxIdentDiff MAXIDENTDIFF]
Parse whole genome alignments for signatures of transposon insertion.
Optional arguments:
-h, --help Show this help message and exit.
-i , --infile An input file containing tab-delimited LASTZ alignment
data.
--outdir Optional: Directory to write output to.
--gffOut Write features to this file as GFF3.
--noflanks If set, do not report flanking hit regions in GFF.
--maxTSD Maximum overlap of insertion flanking sequences in
QUERY genome to be considered as target site
duplication. Flank pairs with greater overlaps will be
discarded Note: Setting this value too high may result
in tandem duplications in the target genome being
falsely classified as insertion events.
--maxInsert The maximum sequence length to consider as an insertion
event.
--minInsert Minimum sequence length to consider as an insertion
event. Note: If too short may detect small non-TE
indels.
--qGap Maximum gap allowed between aligned flanks in QUERY
sequence. Equivalent to target sequence deleted upon
insertion event.
--minIdent Minimum identity for a hit to be considered.
--maxIdentDiff Maximum divergence in identity (to query) allowed
between insert flanking sequences.
License
Software provided under MIT license.
