Provided by: abpoa_1.4.1-3_amd64 bug


       abpoa,  abpoa.avx2,  abpoa.avx,  abpoa.sse4.1,  abpoa.ssse3,  abpoa.sse3,  abpoa.generic -
       adaptive banded Partial Order Alignment


       abpoa [options] <in.fa/fq> > cons.fa/msa.out/abpoa.gfa


       abPOA is an extended version of Partial  Order  Alignment  (POA)  that  performs  adaptive
       banded  dynamic  programming (DP) with an SIMD implementation.  abPOA can perform multiple
       sequence alignment (MSA) on a set of input sequences and generate a consensus sequence  by
       applying the heaviest bundling algorithm to the final alignment graph.

       abPOA  can generate high-quality consensus sequences from error-prone long reads and offer
       significant speed improvement over existing tools.

       abPOA supports three alignment modes  (global,  local,  extension)  and  flexible  scoring
       schemes  that  allow  linear,  affine  and  convex  gap  penalties.  It right now supports
       SSE2/SSE4.1/AVX2 vectorization.



       -m --aln-mode
              INT     alignment mode [0] 0: global, 1: local, 2: extension

       -M --match
              INT     match score [2]

       -X --mismatch
              INT     mismatch penalty [4]

       -t --matrix
              FILE     scoring matrix file, '-M' and '-X' are not used when '-t' is  used  [Null]
              e.g., 'HOXD70.mtx, BLOSUM62.mtx'

       -O --gap-open INT(,INT) gap opening penalty (O1,O2) [4,24]

       -E --gap-ext
              INT(,INT)  gap  extension  penalty  (E1,E2)  [2,1] abPOA provides three gap penalty
              modes, cost of a g-long gap: - convex (default):  min{O1+g*E1,  O2+g*E2}  -  affine
              (set O2 as 0): O1+g*E1 - linear (set O1 as 0): g*E1

       -s --amb-strand
              ambiguous  strand  mode [False] for each input sequence, try the reverse complement
              if the current alignment score is too low, and pick the strand with a higher score

              Adaptive banded DP:

       -b --extra-b
              INT     first adaptive banding parameter [10] set b as  <  0  to  disable  adaptive
              banded DP

       -f --extra-f
              FLOAT      second adaptive banding parameter [0.01] the number of extra bases added
              on both sites of the band is b+f*L, where L is the length of the aligned sequence

              Minimizer-based seeding and partition (only effective in global alignment mode):

       -S --seeding
              enable minimizer-based seeding and anchoring [False]

       -k --k-mer
              INT    minimizer k-mer size [19]

       -w --window
              INT    minimizer window size [10]

       -n --min-poa-win INT
              min. size of window to perform POA [500]

       -p --progressive
              build guide tree and perform progressive partial order alignment [False]


       -Q --use-qual-weight
              take base quality score from FASTQ input file as graph edge weight [False]

       -c --amino-acid
              input sequences are amino acid (default is nucleotide) [False]

       -l --in-list
              input file is a list of sequence file names [False] each line is one sequence  file
              containing  a  set  of  sequences  which  will  be  aligned  by abPOA to generate a
              consensus sequence

       -i --incrmnt
              FILE    incrementally align sequences to an existing graph/MSA [Null]  graph  could
              be in GFA or MSA format generated by abPOA

       -o --output
              FILE    output to FILE [stdout]

       -r --result
              INT    output result mode [0] - 0: consensus in FASTA format - 1: MSA in PIR format
              - 2: both 0 & 1 - 3: graph in GFA format - 4: graph  with  consensus  path  in  GFA
              format - 5: consensus in FASTQ format

       -d --maxnum-cons INT
              max. number of consensus sequence to generate [1]

       -q --min-freq
              FLOAT      min.   frequency   of  each  consensus  sequence  (only  effective  when
              -d/--num-cons > 1) [0.25]

       -g --out-pog
              FILE    dump final alignment graph to FILE (.pdf/.png) [Null]

       -h --help
              print this help usage information

       -v --version
              show version number


       For more information please refer to the paper published in Bioinformatics: