---
name: "parasail_aligner"
section: "1"
platform: "linux"
package: "parasail"
version: "2.6.2+dfsg-2"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/parasail_aligner"
---

# parasail\_aligner(1)

Development heaaders and static libraries for parasail

## 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.