ATAC(1)

💖 ATAC(1) — General Commands Manual 💖

okay bestie, pull up a chair, because we're talking about atac — comparative mapping between genome sequences 🧬✨ it's giving big-brain bioinformatics and honestly? iconic.

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🌸 NAME 🌸

atac — comparative mapping between genome sequences 🦋

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✨ SYNOPSIS ✨

atac -meryldir alignment_cache_dir -dir result_dir -id1 seqid1
-seq1 seqfile1.fasta -id2 seqid2 -seq2 seqfile2.fasta

like yes, that's the whole vibe. copy it, don't freestyle it 💅

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🧚 DESCRIPTION 🧚

okay so here's the tea ☕ — atac computes a one-to-one pairwise alignment of large DNA sequences. no cap.

the way it works is honestly so satisfying:

1. first it finds the unique k-mers in each sequence 🔍
2. then it chains them into larger blocks 🔗
3. then it fills in the spaces between blocks 🫶

and why does this exist? because it was written primarily to transfer annotations between different assemblies of the human genome. main character origin story fr fr 👑

the output is a set of ungapped 'matches', plus a set of gapped 'runs' formed from the matches. each match or run associates one sequence with the other sequence. and here's the key part — the association is 'unique', meaning there is no other (sizeable) associations for either sequence. so basically, large repeats and duplications are not present in the output — they show up as unmapped regions instead. periodt 💀

and even though the output is always pairwise, atac can cache intermediate results to speed up comparisons of multiple sequences. efficiency queen 🌈

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💅 OPTIONS 💅

• Run with no options for a list of parameters. — literally just run it with nothing and it'll spill all the deets for you, no gatekeeping 🙈

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🎀 SEE ALSO 🎀

• leaff(1) 🌿
• /usr/share/doc/atac/README.atac 📄
• http://kmer.sourceforge.net/wiki/index.php/Getting_Started_with_ATAC 🌐

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and that's the whole page bestie, go align something gorgeous ✨

this little manual moment was brought to you by the ATAC(1) page, dated November 2016 🗓️ — old but gold, and still serving 💖🦋⭐