Please Note: Fix start and orientation requires the Long Read Data Analysis Module
This function searches for possible starting points of replication within chromosomes and plasmids and re-orients the FASTA files so that the sequences start at the found starting point. It searches using BLAST for matches with a dnaA-library for chromososmes and for matches with a rep-library for plasmids. The decision whether a contig is a plasmid or a chromosome is based on the size of the contig: Contigs from 3000 to 500,000 bases are considered plasmids, larger contigs are considered chromosomes. All contigs shorter than 500 bases are ignored.
By default the functions assumes that the contigs and plasmids are circular. If the box Look for [topology=circular] tag in FASTA contig header instead assuming that contig(s) are circular is checked, the topology is decided by the presence of the [topology=circular] tag in the contig name. Selecting the box Skip non-circular contigs allows to leave contigs without the [topology=circular] tag unchanged.
If a hit is found and the contig is circular, the contig is rotated so that it starts at that hit. If the hit is in inverse direction, the reverse complement of the sequence is used. The tag [fixed] is added to the contig name. If a hit is found and the contig is not circular, the contig is split into two contigs at that hit. If the hit is in inverse direction, the reverse complement of the sequence is used. The tag [split] is added to the first contig name, the tag [fixed] is added to the second contig name.
If multiple hits are found, the hits that contain rep_cluster in their name are sorted to the end. Afterwards, the best hit is used. If the best hit begins within the first 50 bases of the contig no changes are made.
Note that this function is useful only for data with complete contigs and plasmids (e.g. long-read data).
A file or a directory can be used for input. If a directory is used, all files with a FASTA-file ending are processed.
Files in the output directory may be overwritten.
Used libraries
for dnaA: dnaA-library (amino acid) from Circlator
for rep: rep-library (nucleotide ) from Mob-Suite