Instructions are sequentially executed and each instruction is described by tab-separated columns.
The JOIN instruction introduces a new gap of 50 bp between scaffold1 and scaffold2 (two paths) with id gap1, effectively joining the two sequences into a new sequence with id new_scaffold and an optional comment.
JOIN scaffold1+ scaffold2+ 50 gap1 new_scaffold
JOIN scaffold1(1:100)+ scaffold2(1:100)+ 50 gap1 new_scaffold // optional subsetting
The SPLIT instruction splits the scaffold containing segment1 and segment2, effectively removing the existing gap between them. Two optional comments can be provided.
SPLIT segment1+ segment2+ scaffold1 scaffold2 [this is a new scaffold1] [this is a new scaffold2]
The EXCISE instruction removes segment1 from its scaffold, leaving it unplaced and adding a gap of 50bp with id gap1 between the original sequences
EXCISE segment1 50 gap1
The REMOVE instruction removes the paths involving the specified segment.
REMOVE segment1
The EXCLUDE instruction removes the specified path and all its components.
EXCLUDE path1
The ERASE instruction trims off the sequence range specified from the given segment.
ERASE segment1:10-100 // deletes segment1 sequence between the coordinates provided (in bed format)
The RVCP instruction reverse-complements path1 or segment1 sequence in place
RVCP path1/segment1
The INVERT instruction inverts segment1 sequence in place
INVERT segment1
The RESIZE instruction resizes the size of gap1 to 50 bp
RESIZE gap1 50
The MASK instruction masks with 50 Ns a portion of a path, effectively adding a gap in the corresponding segment of optional size 5. If size is not provided, the masked size is used
MASK path1 10 60 [5]
The CLEAVE instruction breaks the specified segment at the given position generating segment2 and segment3, optionally connected by an edge
CLEAVE segment1 50 segment2 segment3 [edge1]
ADD contig3 contig1+ 50 contig2+ 50 ACGT // introduces a new contig named contig3 with sequence ACGT between contig1 and contig2 leaving 50bp gaps on each side
REPLACE contig1:20-24 ACGT // replaces the sequence at coordinates contig1:20-24 with ACGT