TRAIN(1)

💖 NAME 💖

train — interpretation of DNA Sanger sequencing data 🧬✨

🌸 DESCRIPTION 🌸

okay bestie, so train is out here doing the absolute most with your DNA Sanger sequencing data, and the way it takes its orders is entirely through flags. no positional args, no drama, just vibes and options. here's the full lineup, no skips, no cuts 👑:

• -h — (Help) this message. she's the "hey what do I even do" button 🫶
• -nocall — Disable base recalling and just use the original called bases read from the input sample file. like, don't touch it, it's already iconic 💅
• -recalln — Disable adding bases to or deleting from the original called sequence. Only recall Ns. N-only glow-up, nothing else moves 🙈
• -recallndb — Disable adding bases to or deleting from the original called sequence. Only recall Ns and dye blobs. so Ns and dye blobs get the attention, still no add/delete energy 💀
• -ladder — Similar to -recalln, but all bases, not only Ns will be recalled from original locations. everybody gets recalled, not just the Ns, fr fr 🌈
• -edited_bases — Start base recalling from the ABI's edited bases. we're trusting the ABI's own edits as the starting point, periodt ✨
• -het — Call heterozygous bases. two alleles walked in, so we say both 👑
• -mix — Call mixed bases. mixed bases get their moment too 🎀
• -min_ratio <ratio> — Override the default threshold ratio of heights of the lowest peak to the highest peak at a given position. you're the boss of that ratio now 💅
• -fr <repeat_fraction> — Specify the repeat_fraction. the default is 0.85 ⭐
• -fe <max_frac_of_err> — Specify the allowable fraction of errors within the best alignment region. Default is 0.1. If actual fraction of errors exceeds this vale, the fragment will be rejected (=not used in training process). so if your error fraction pops off past this, the fragment gets benched and doesn't get used in training 😭 (yes, "vale" is a typo in the original and yes we're keeping it, character for character, no notes)
• -o <output_file> — Specify the name of the output file. By default, the output will be made to stdout. main character output destination energy 👑
• -C <consensusfile> — Specify the name of the FASTA file which contains the consensus sequence. consensus? in this FASTA file? more likely than you think 🦋
• -V <vector> — Specify the name of the FASTA file which contains the vector sequence 🧬
• -P <primer> — Specify the name of the FASTA file which contains the primer sequence 🍓
• -S <site> — Specify the name of the FASTA file which contains the restriction site sequence ✂️
• -M <match> — Specify the match premium. the default is 10 💖
• -X <mismatch> — Specify the mismatch penalty. the default is 20 💀
• -G <gap_penalty > — Specify the gap initiation or extension penalty. the default is 40 🫶
• -d <dir> — Read the input sample files from specified directory. tell her where the samples live and she'll go get them 🧚
• -p <projectfile> — Specify the name of the projectfile which consists of two columns. Each line in this file contains the full path to the sample file to be processed and the full path to the FASTA file which contains the consensus sequence that should be used with this sample file. two columns, one line per sample, sample path + its consensus FASTA path, and that's the whole assignment ✨

ngl the flag list is long but every single one of them is doing a job. no filler, no skips, all facts preserved, iykyk 💜

🌈 AUTHOR 🌈

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program. shoutout to Andreas, absolute legend 🫶👑

and that's the whole page bestie!! 💅 this was train version 3.0.6~beta, dated October 2018, in the User Commands manual — thanks for reading, go slay your sequencing data 🎀✨🦋