UC-ECHO(1)

💖 NAME 💖

okay so bestie, meet uc-echo — it does Short-read Error Correction ✨ that's literally the whole vibe. it's a User Commands girlie from the uc-echo(1) manual, and she is here to fix your reads. periodt. 🧚

🌸 SYNOPSIS 🌸

the whole shape of it, no notes:

uc-echo [options] read_file_name

so you hand her some [options], you hand her a read_file_name, and she goes to work. that's it. that's the summoning ritual 🫶

✨ OPTIONS ✨

🎀 round one (yes, there are two rounds, we'll get there)

• -h, --help — shows you this very help message and then dips. exit time. 👋
• -o OUTPUT_FILENAME, --output=OUTPUT_FILENAME — names the output file. give ur baby a name 💖
• -l LOG_FILENAME, --log=LOG_FILENAME — names the log file. receipts, but make them a file 📝
• --DD=TMP_DIRECTORY, --tmp_dir=TMP_DIRECTORY — where the temporary data lives. the lil stash spot 🗂️
• -u NCPU, --ncpu=NCPU — how many processes get used during training. more hands, more work 🫶
• -b BSIZE, --block_size=BSIZE — splits the data into blocks of the size you specify. chunk it up 🍫
• --nh=NHASH, --n_hash_block=NHASH — splits the hash table into n tables. dividing the group chat into side chats 💬
• --rm=READ_MERGE, --read_merge_size=READ_MERGE — merges n hash tables at a time. slay, consolidate 💅
• --hm=HASH_MERGE, --hash_merge_batch_size=HASH_MERGE — merges n adjacency lists at a time. same energy, different list 🔥
• -k K, --kmer=K — the k-mer size used for hashing. the K matters, don't be random about it ⭐
• -e E, --min_error_tolerance=E — the minimum error tolerance for parameter searching. the floor 🦋
• -E E, --max_error_tolerance=E — the maximum error tolerance for parameter searching. the ceiling 🌈
• --hh=H, --min_minimum_overlap=H — the minimum minimum overlap length for parameter searching. yes it says minimum twice, that's not a typo, that's just her 🫠
• --hH=H, --max_minimum_overlap=H — the maximum minimum overlap length for parameter searching. the other end of the same situationship 😭
• --h_rate=H_RATE, --heterozygous_rate=H_RATE — the rate for a heterozygous site. genetics said hi 🧬
• --model_selection_size=MSIZE — the model selection data set size. how much data gets a say in the model choosing 👑
• --keep_all_files — keeps all temporary files. by default, temporary files are deleted automatically, so this is you saying "no bestie, keep everything" 🙈

🦋 round two (the original really does list them all over again, so here we go, no skips)

• -h, --help — shows you this help message and exits. encore performance 🎤
• -o OUTPUT_FILENAME, --output=OUTPUT_FILENAME — the output file name. same icon, second appearance 💫
• -l LOG_FILENAME, --log=LOG_FILENAME — the log file name. the log stays logging 📓
• --DD=TMP_DIRECTORY, --tmp_dir=TMP_DIRECTORY — the temporary data directory. temp files, temp home 🏠
• -u NCPU, --ncpu=NCPU — number of processes used in training. say it again for the people in the back 🗣️
• -b BSIZE, --block_size=BSIZE — split data into blocks of the specified size. blocks on blocks 🧱
• --nh=NHASH, --n_hash_block=NHASH — split the hash table into n tables. hash girlies rise 💅
• --rm=READ_MERGE, --read_merge_size=READ_MERGE — merge n hash tables at a time. merge szn 🔗
• --hm=HASH_MERGE, --hash_merge_batch_size=HASH_MERGE — merge n adjacency lists at a time. batch it up 🎁
• -k K, --kmer=K — k-mer size used for hashing. K is K ⭐
• -e E, --min_error_tolerance=E — minimum error tolerance for parameter searching. lowkey the lower bound 🦋
• -E E, --max_error_tolerance=E — maximum error tolerance for parameter searching. highkey the upper bound 🌈
• --hh=H, --min_minimum_overlap=H — minimum minimum overlap length for parameter searching. she said it twice and she meant it twice 😭
• --hH=H, --max_minimum_overlap=H — maximum minimum overlap length for parameter searching. iconic naming choices, honestly 👑
• --h_rate=H_RATE, --heterozygous_rate=H_RATE — rate for heterozygous site. biology bestie 🧬
• --model_selection_size=MSIZE — model selection data set size. the model gets a data set to be judged by 💖
• --keep_all_files — keep all temporary files. by default, temporary files are deleted automatically, and that default has not changed, no cap 💀

heads up bestie: in the original, the option list genuinely appears twice, start to finish. i didn't merge them, rename them, or "fix" anything — every flag is listed here exactly as many times as she listed it. that's the assignment and we did it 🫡

and that's the whole page, bestie. this one's uc-echo, dated April 2013, and it's a UC-ECHO(1) girl through and through. go correct some reads. slay. 💅✨🎀