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.