Shore preprocess

shore preprocess creates the mapping indices, calculates local GC content and sequence complexity. In addition, SHORE will create a new copy of the fasta file of the reference sequence featuring adjusted chromosome/contig ids and write all files to the IndexFolder.

Usage: shore preprocess [OPTIONS] [FASTA_FILES]

Mandatory
-f, --fastafile=<arg[,...]>		Fasta file(s) containing all reference sequences
-i, --indexfolder=<arg>		IndexFolder. Output folder for all SHORE relevant files.
Mapping indices
-s, --seed=<arg[,...]>	(Default: 12)	Seedlength(s) for mapping indices (5-13)
-b, --bowtie		Activate Bowtie support
-n, --novo		Activate Novocraft novoalign support
-e, --eland		Activate Eland support
-p, --gsnap		Activate GSNAP support
-t, --blat		Activate blat support
-W, --bwa		Activate BWA support
--bwa-construction-algorithm=<arg>	(Default: is)	BWA construction algorithm. Possible options are: is (up to 2GB databases), bwtsw (databases larger than 10MB). For further details see 'bwa index'.
-U, --ssuff		Activate internal suffix array indexing
-g, --no-genomemapper		Inactivates GenomeMapper
BS-Seq (bisulfite treated DNA)
-B, --bsseq		Turns on indexing for BS-seq experiments. Only genomemapper and novo are supported. BS-seq indices are calculated in addition to the normal indices for genomemapper and novo.
Sequence complexity
-c, --complexity=<arg>	(Default: 9)	Window size in bp for sequence complexity analysis
-w, --gccontent=<arg>	(Default: 101)	Odd window size in bp for GC content measuring
SOLiD support
-C, --build-colorspace-index		Build color-space index
GenomeMapper Graph version support
-V, --variation-files=<arg>		Variation file(s) (comma separated absolute paths). Turns on graph version
Other Options
--maxsize=<arg>		Split into multiple indeces if the sequences exceed this size in megabytes
--headers		Include the complete fasta headers in the *.trans file (default is first word)