PARASAIL_ALIGNER(1)

💖 PARASAIL_ALIGNER(1) 💖

okay bestie, sit down, hydrate, and let me tell you about parasail_aligner — it's a User Command, it's iconic, and it's literally here to do your sequence alignments for you. 🦋

✨ NAME ✨

parasail_aligner — Development heaaders and static libraries for parasail

ngl bestie, "heaaders" is spelled exactly like that in the original and I am not touching it, that's the vibe we're preserving fr fr 💅

🌸 DESCRIPTION 🌸

so here's the whole tea. the usage is giving:

usage: parasail_aligner [-a funcname] [-c cutoff] [-x] [-e gap_extend] [-o gap_open] [-m matrix] [-t threads] [-d] [-M match] [-X mismatch] [-k band size (for nw_banded)] [-l AOL] [-s SIM] [-i OS] [-v] [-V] -f file [-q query_file] [-g output_file] [-O output_format {EMBOSS,SAM,SAMH,SSW}] [-b batch_size] [-r memory_budget] [-C] [-A alphabet_aliases]

like, look at all those flags. she has range. 🎀

🌈 Defaults:

here's where it gets juicy, because every single one of these has a default and a rule, and you will respect the rules:

• funcname — sw_stats_striped_16
• cutoff — 7, must be >= 1, exact match length cutoff
• -x — if present, don't use suffix array filter
• gap_extend — 1, must be >= 0
• gap_open — 10, must be >= 0
• matrix — blosum62
• -d — if present, assume DNA alphabet ACGT
• match — 1, must be >= 0
• mismatch — 0, must be >= 0
• threads — system-specific default, must be >= 1
• AOL — 80, must be 0 <= AOL <= 100, percent alignment length
• SIM — 40, must be 0 <= SIM <= 100, percent exact matches
• OS — 30, must be 0 <= OS <= 100, percent optimal score over self score
• -v — verbose output, report input parameters and timing
• -V — verbose memory output, report memory use
• file — no default, must be in FASTA format
• query_file — no default, must be in FASTA format
• output_file — parasail.csv
• output_format — no default, must be one of {EMBOSS,SAM,SAMH,SSW}
• batch_size — 0 (calculate based on memory budget), how many alignments before writing output
• memory_budget — 2GB or half available from system query (4.046 GB)
• -C — if present, use case sensitive alignments, matrices, etc.
• alphabet_aliases — traceback will treat these pairs of characters as matches, for example, 'TU' for one pair, or multiple pairs as 'XYab'

👑 AUTHOR 👑

This manpage was written by Nilesh Patra for the Debian distribution and can be used for any other usage of the program.

and that's the whole page bestie, no cap. 💜

this was parasail_aligner 2.4.1, from April 2020, living its best PARASAIL_ALIGNER(1) life. go align something slay. 🧚✨🫶