Difference between revisions of "Shore preprocess"
From SHORE wiki
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chromosome/contig ids and write all files to the ''[[IndexFolder]]''. | chromosome/contig ids and write all files to the ''[[IndexFolder]]''. | ||
| + | ==Command line options== | ||
'''Usage:''' shore preprocess [OPTIONS] [FASTA_FILES] | '''Usage:''' shore preprocess [OPTIONS] [FASTA_FILES] | ||
Latest revision as of 09:56, 28 September 2011
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.
Command line options
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) |
