Where are Insertion Sequences
A package to find where the insertion sequences (IS) are located in a reference genome, or an assembly - using short-read sequences. Additional to finding the point of insertion, the orientation of the insertion and the IS type is also reported.
Installation instructions are here.
Required parameters:
--outputDir
--ISseqs
--reads_1
--reads_2 And, one of the following:
--runSpades
--assembly# Invoke help
python3 wais.py --help
# When you have already assembled the reads (we recommend using SPAdes, it takes longer than SKEASA, but provides higher accuracy for identifying IS insertions).
python3 wais/wais.py --outputDir SRR9988840 --ISseqs Example/IS_seqs_found_in_BP.fasta --reads_1 Example/SRR9988840_1.fastq.gz --reads_2 Example/SRR9988840_2.fastq.gz --assembly Example/contigs.fasta
# Alternatively, also run spades with WaIS.
python3 ...
# Map the identified insertions to a reference genome.
python3 ...