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parasail_aligner - Development heaaders and static libraries for parasail


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]


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
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'


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

April 2020 parasail_aligner 2.4.1