Defaults:¶

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'