NAME

       chimeraslayer - detects likely chimeras in PCR amplified DNA

DESCRIPTION

       ChimeraSlayer  is  a chimeric sequence detection utility, compatible with near-full length
       Sanger sequences and shorter 454-FLX sequences (~500bp).

       Chimera Slayer involves the following series of steps that operate to  flag  chimeric  16S
       rRNA sequences:

       1.     the ends of a query sequence are searched against an included database of reference
              chimera-free 16S sequences to identify potential parents of a chimera

       2.     candidate parents of a chimera are selected as those  that  form  a  branched  best
              scoring alignment to the NAST-formatted query sequence

       3.     the  NAST alignment of the query sequence is improved in a ‘chimera-aware’ profile-
              based NAST realignment to the selected reference parent sequences

       4.     an evolutionary framework is used to flag query sequences found to exhibit  greater
              sequence  homology  to  an in silico chimera formed between any two of the selected
              reference parent sequences.

       To run Chimera Slayer,  you  need  NAST-formatted  sequences  generated  by  the  nast-ier
       utility.

       ChimeraSlayer is part of the microbiomeutil suite.

OPTIONS

   Required
       --query_NAST
              multi-fasta file containing query sequences in alignment format

   Common options
       --db_NAST
              db               in               NAST               format               (default:
              /usr/share/microbiomeutil-data/RESOURCES/rRNA16S.gold.NAST_ALIGNED.fasta)

       --db_FASTA
              db      in      fasta      format       (megablast       formatted)       (default:
              /usr/share/microbiomeutil-data/RESOURCES/rRNA16S.gold.fasta)

       -n     number of top matching database sequences to compare to (default 15)

       -R     min divergence ratio default: 1.007

       -P     min percent identity among matching sequences (default: 90)

   Parameters to tune ChimeraParentSelector:
       Scoring parameters:

       -M     match score   (default: +5)

       -N     mismatch penalty  (default: -4)

       -Q     min query coverage by matching database sequence (default: 70)

       -T     maximum traverses of the multiple alignment  (default: 1)

   Parameters to tune ChimeraPhyloChecker
       --windowSize
              default 50

       --windowStep
              default 5

       --minBS
              minimum bootstrap support for calling chimera (default: 90)

       --num_BS_replicates
              default: 100

       --low_range_finer_BS
              (default:  10)  If  computed  BS is between minBS and (minBS - low_range_finer_BS),
              then num_finer_BS_replicates computed.

       --num_finer_BS_replicates
              (default: 1000)

       -S     percent of SNPs to sample on  each  side  of  breakpoint  for  computing  bootstrap
              support (default: 10)

       --num_parents_test
              number of potential parents to test for chimeras (default: 3)

       --MAX_CHIMERA_PARENT_PER_ID
              Chimera/Parent  alignments  with  perID  above  this  are  considered  non-chimeras
              (default 100; turned off)

   Misc options
       --printFinalAlignments
              shows alignment between query sequence and pair of candidate chimera parents

       --printCSalignments
              print ChimeraSlayer alignments in ChimeraSlayer output

       --exec_dir
              chdir to here before running

SEE ALSO

       http://microbiomeutil.sourceforge.net/#A_CS

AUTHOR

       This manual page was written by Andreas Tille <tille@debian.org> but can  be  freely  used
       for any other distribution.