PBDAGCON(1)

💖 PBDAGCON(1) 💖

okay bestie, so this is a General Commands Manual page, and honestly? it's giving bioinformatics royalty. it's pbdagcon, and we're about to make consensus sequences make sense. 🧬✨

🌸 NAME 🌸

pbdagcon — sequence consensus using directed acyclic graphs

like, it does consensus. with DAGs. we love a niche queen. 👑

🦋 DESCRIPTION 🦋

so pbdagcon is the tool that runs DAGCon (aka Directed Acyclic Graph Consensus), which is a sequence consensus algorithm built on using directed acyclic graphs to encode multiple sequence alignment. no cap. 💅

it takes the alignment info from blasr(1) and uses it to align sequence reads to a "backbone" sequence. then, based on the underlying alignment DAG, it can use the new info from those reads to find the discrepancies between the reads and the "backbone" sequences. after that, a dynamic programming process gets applied to the DAG to find the optimum sequence of bases — that's your consensus. 🔥 and here's the slay part: that new consensus can be used as a new backbone sequence to iteratively improve the consensus quality. glow-up after glow-up, literally. ✨

now, the code was developed for processing PacBio(TM) raw sequence data, but the algorithm can be used for general consensus purpose too — she's versatile, she contains multitudes. currently, it only takes FASTA input. and for shorter read sequences, one might need to adjust the blasr(1) alignment parameters to get the alignment string properly. consider that your little heads-up, bestie. 🫶

the code and the underlying graphical data structure have also been used for some algorithm development prototyping, including:

• phasing reads
• pre-assembly
• a work around to generate consensus from intermediate Celera Assembler outputs

not her being a whole research side quest. iconic behavior. 🎀

⭐ OPTIONS ⭐

a summary of options is available from the program's help menu. (yes, that's the whole vibe of this section. she's mysterious. iykyk.)

• --help — show summary of options. the classic. the icon. ask her and she'll tell you everything. 🌈

👀 SEE ALSO 👀

• blasr(1)
• /usr/share/doc/pbdagcon/examples

go peek at the examples folder, it's lowkey the lore drop you need. 💜

okay and finally, the cute little sign-off at the bottom of the page: this manual is from December 2015, and it's the PBDAGCON(1) page itself — so that's the source/version and the date, bestie. 💖 thanks for reading, go generate some consensus, mwah! 🦋🎀💅