Provided by: abpoa_1.5.3-1build2_amd64 
NAME
abpoa, abpoa.avx2, abpoa.avx, abpoa.sse4.1, abpoa.ssse3, abpoa.sse3, abpoa.generic - adaptive banded
Partial Order Alignment
SYNOPSIS
abpoa [options] <in.fa/fq> > cons.fa/msa.fa/abpoa.gfa
DESCRIPTION
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.
OPTIONS
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]
SEE ALSO
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)