NAME

       sumatra - fast and exact comparison and clustering of sequences

SYNOPSIS

       sumatra [options] <dataset1> [dataset2]

DESCRIPTION

       Sumatra  computes  all  the  pairwise  LCS  (Longest  Common  Subsequence)  scores  of one
       nucleotide dataset or between two nucleotide datasets.

OPTIONS

       -h     [H]elp - print <this> help

       -l     Reference sequence length is the shortest.

       -L     Reference sequence length is the largest.

       -a     Reference sequence length is the alignment length (default).

       -n     Score is normalized by reference sequence length (default).

       -r     Raw score, not normalized.

       -d     Score is expressed in distance (default: score is expressed in similarity).

       -t ##.##
              Score threshold. If the score is normalized and expressed in similarity  (default),
              it is an identity, e.g. 0.95 for an identity of 95%. If the score is normalized and
              expressed in distance, it is (1.0 - identity), e.g. 0.05 for an  identity  of  95%.
              If the score is not normalized and expressed in similarity, it is the length of the
              Longest Common Subsequence. If  the  score  is  not  normalized  and  expressed  in
              distance, it is (reference length - LCS length).
              Only  sequence  pairs  with a similarity above ##.## are printed. Default: 0.00 (no
              threshold).

       -p ##  Number of threads used for computation (default=1).

       -g     n's are replaced with a's (default: sequences with n's are discarded).

       -x     Adds four extra columns with the count and length of both sequences.

       dataset1
              (First argument) the nucleotide dataset to analyze

       dataset2
              (Second argument) optionally the second nucleotide dataset

RESULTS

       Results table description
       column 1 : Identifier sequence 1
       column 2 : Identifier sequence 2
       column 3 : Score
       column 4 : Count of sequence 1  (only with option -x)
       column 5 : Count of sequence 2  (only with option -x)
       column 6 : Length of sequence 1 (only with option -x)
       column 7 : Length of sequence 2 (only with option -x)

SEE ALSO

       http://metabarcoding.org/sumatra