PARASAIL_ALIGNER

NAME

parasail_aligner - Development heaaders and static libraries for parasail

DESCRIPTION

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]

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’

AUTHOR

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