NAME

       RazerS - Fast Read Mapping with Sensitivity Control

SYNOPSIS

       razers [OPTION]... <GENOME FILE> <READS FILE>

DESCRIPTION

       RazerS - Fast Read Mapping with Sensitivity Control

              razers [OPTION]... <GENOME FILE> <MP-READS FILE1> <MP-READS FILE2>

       -h,  --help
              displays this help message

       -V,  --version
              print version information

   Main Options:
       -f,  --forward
              only compute forward matches

       -r,  --reverse
              only compute reverse complement matches

       -i,  --percent-identity NUM
              set the percent identity threshold (default 92)

       -rr, --recognition-rate NUM
              set the percent recognition rate (default 99)

       -pd, --param-dir DIR
              folder containing user-computed parameter files (optional)

       -id, --indels
              allow indels (default: mismatches only)

       -ll, --library-length NUM
              mate-pair library length (default 220)

       -le, --library-error NUM
              mate-pair library length tolerance (default 50)

       -m,  --max-hits NUM
              output only NUM of the best hits (default 100)

       --unique
              output only unique best matches (-m 1 -dr 0 -pa)

       -tr, --trim-reads NUM
              trim reads to given length (default off)

       -o,  --output FILE
              change output filename (default <READS FILE>.result)

       -v,  --verbose
              verbose mode

       -vv, --vverbose
              very verbose mode

   Output Format Options:
       -a,  --alignment
              dump the alignment for each match

       -pa, --purge-ambiguous
              purge reads with more than max-hits best matches

       -dr, --distance-range NUM
              only  consider  matches  with at most NUM more errors compared to the best (default
              output all)

       -of, --output-format NUM
              set output format (default 0) 0 = Razer format 1 = enhanced Fasta format 2 =  Eland
              format 3 = GFF format

       -gn, --genome-naming NUM
              select  how  genomes are named (default 0) 0 = use Fasta id 1 = enumerate beginning
              with 1

       -rn, --read-naming NUM
              select how reads are named (default 0) 0 = use Fasta id  1  =  enumerate  beginning
              with 1 2 = use the read sequence (only for short reads!)

       -so, --sort-order NUM
              select  how matches are sorted (default 0) 0 = 1. read number, 2. genome position 1
              = 1. genome position, 2. read number

       -pf, --position-format NUM
              select begin/end position numbering (default 0) 0 = gap space 1 = position space

   Filtration Options:
       -s,  --shape BITSTRING
              set k-mer shape (default 11111111111)

       -t,  --threshold NUM
              set minimum k-mer threshold (default 1)

       -oc, --overabundance-cut NUM
              set k-mer overabundance cut ratio (default 1)

       -rl, --repeat-length NUM
              set simple-repeat length threshold (default 1000)

       -tl, --taboo-length NUM
              set taboo length (default 1)

   Verification Options:
       -mN, --match-N
              'N' matches with all other characters

       -ed, --error-distr FILE
              write error distribution to FILE

AUTHOR

       razers was written by David Weese.

       This  manual  page  was  generated  using  html2man  and  polished  by  Soeren  Sonnenburg
       <sonne@debian.org>, for the Debian project (but may be used by others).