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

       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.

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

              Alignment:

       -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]

              Input/Output:

       -Q--use-qual-weight
              take  base  quality score from FASTQ input file as graph edge weight for consensus calling [False]
              effective only when input sequences are in  FASTQ  format  and  consensus  calling  with  heaviest
              bundling

       -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

       -a--cons-algrm INT
              consensus algorithm [0] - 0: heaviest bundling path in partial order  graph  -  1:  most  frequent
              bases at each position

       -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

       -V--verbose
              INT    verbose level (0-2). 0: none, 1: information, 2: debug [0]

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

       https://dx.doi.org/10.1093/bioinformatics/btaa963

abpoa 1.5.3                                      September 2024                                         ABPOA(1)

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