ABPOA(1)

✨ ABPOA(1) — bestie, let's talk about abpoa 💖

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 💅

okay so abPOA is an extended version of Partial Order Alignment (POA) and it is giving adaptive banded dynamic programming (DP) with an SIMD implementation 🔥. It can do multiple sequence alignment (MSA) on a whole set of input sequences and then spit out a consensus sequence by running the heaviest bundling algorithm on the final alignment graph 👑.

ngl it makes high-quality consensus sequences out of error-prone long reads, and it's significantly faster than existing tools. iconic 😭✨

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

🎀 OPTIONS 🎀

Alignment:

• -m, --aln-mode — alignment mode, an INT, defaults to 0. 0 is global, 1 is local, 2 is extension 🌈
• -M, --match — match score, an INT, defaults to 2 💜
• -X, --mismatch — mismatch penalty, an INT, defaults to 4 💀
• -t, --matrix — a FILE holding a scoring matrix. When -t is used, -M and -X are ignored. No default (Null). Examples: HOXD70.mtx, BLOSUM62.mtx 🍓
• -O, --gap-open — gap opening penalty (O1,O2), takes INT(,INT), defaults to [4,24] 🦋
• -E, --gap-ext — gap extension penalty (E1,E2), takes INT(,INT), defaults to [2,1] ✨

The gap penalty modes are the main event here 🫶. 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, defaults to False. For each input sequence, if the current alignment score is too low, it tries the reverse complement and keeps whichever strand scores higher 🔄

Adaptive banded DP:

• -b, --extra-b — first adaptive banding parameter, an INT, defaults to 10. Set b to a value < 0 to turn adaptive banded DP off 🙈
• -f, --extra-f — second adaptive banding parameter, a FLOAT, defaults to 0.01. The number of extra bases added on both sides 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 — turn on minimizer-based seeding and anchoring, defaults to False 🌟
• -k, --k-mer — minimizer k-mer size, an INT, defaults to 19 🔥
• -w, --window — minimizer window size, an INT, defaults to 10 🌈
• -n, --min-poa-win — min. size of window to perform POA, an INT, defaults to 500 🎀
• -p, --progressive — build a guide tree and do progressive partial order alignment, defaults to False 👑

Input/Output:

• -Q, --use-qual-weight — take base quality scores from the FASTQ input file and use them as graph edge weights for consensus calling. Defaults to False. Only works when the input is FASTQ and you're doing consensus calling with heaviest bundling 🧚
• -c, --amino-acid — input sequences are amino acid instead of nucleotide (nucleotide is the default), defaults to False 🍓
• -l, --in-list — the input file is a list of sequence file names, defaults to False. Each line is one sequence file holding a set of sequences, and abPOA aligns them all to make a consensus 💅
• -i, --incrmnt — a FILE to incrementally align sequences onto an existing graph or MSA, defaults to Null. The graph can be GFA or MSA format, as long as abPOA made it 🦋
• -o, --output — write output to a FILE, defaults to stdout ✨
• -r, --result — output result mode, an INT, defaults to 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 — consensus algorithm, an INT, defaults to 0:
  • 0: heaviest bundling path in partial order graph
  • 1: most frequent bases at each position
• -d, --maxnum-cons — max. number of consensus sequences to generate, an INT, defaults to 1 🌸
• -q, --min-freq — min. frequency of each consensus sequence, a FLOAT, defaults to 0.25. Only does something when -d/--num-cons is greater than 1 🫶
• -g, --out-pog — dump the final alignment graph to a FILE (.pdf or .png), defaults to Null 🎀
• -h, --help — print the help usage info 💖
• -v, --version — show the version number ✨
• -V, --verbose — verbose level, an INT from 0 to 2, defaults to 0. 0 is none, 1 is information, 2 is debug 🙈

🦋 SEE ALSO 🦋

okay bestie, for more info check out the paper published in Bioinformatics:

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

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abpoa 1.5.3, September 2024: that's the version and date stamp, lowkey iconic. Stay gorgeous, Unix queen 👑🫶💅✨