ins

The ins tool is a repeat identification/annotation tool.

ins takes a query sequence (usually a genome) and a library or set of FASTA libraries of know repeat sequences. It uses nucleotide BLAST+ to find instances of the repeats in the library within the query sequence and outputs a copy of the sequence with the identified repeats masked with N. The locations of repeats are output on standard output in either GTF format or as a JSON stream. Logging is made to standard error.

Installation

The ins program can be installed after installing the Go programming language.

$ go get github.com/kortschak/ins/cmd/ins

ins requires that the NCBI+ BLAST distribution is installed on your system and that blastn and makeblastdb are in your $PATH.

Usage

$ ins [options] -lib <library.fa> [-lib <library.fa> ...] -query <seq.fa> >out.gtf 2>out.log

or

$ ins [options] -json -lib <library.fa> [-lib <library.fa> ...] -query <seq.fa> >out.json 2>out.log

For expert users, additional or alternative flags may be passed to makeblastdb and blastn using the -mflags and -bflags options. Users of -mflags and -bflags must not re-set flags that have already been set by ins; these will always include

• makeblastdb
  • -in
  • -out
  • -dbtype
• blastn
  • -db
  • -query
  • -outfmt

A variety of other flags are set when running blastn

• -evalue
• -word_size
• -dust
• -soft_masking
• -reward
• -penalty
• -xdrop_ungap
• -xdrop_gap
• -xdrop_gap_final
• -gapopen
• -gapextend
• -num_alignments
• -searchsp
• -parse_deflines
• -num_threads

If a user intends to re-set these an empty configuration mode must be selected by using -mode=user in addition to the -bflags option. The requirement may be relaxed in future. When using the user mode, all necessary flags must be provided via the -bflags option.