Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Parameters for multi-threads? #21

Closed
zhaotao1987 opened this issue Nov 15, 2021 · 1 comment
Closed

Parameters for multi-threads? #21

zhaotao1987 opened this issue Nov 15, 2021 · 1 comment

Comments

@zhaotao1987
Copy link

zhaotao1987 commented Nov 15, 2021

Hi! @mawad89 GALA seems powerful, I'm trying this software out.. however I don't see a parameter for multi-threads(?).
For example, running bwa takes pretty long if not multi-threaded. Thanks!

usage: gala -h [options] <draft_names & paths> <fa/fq>

GALA Gap-free Long-reads Assembler

positional arguments:
draft_names Draft names and paths [required]
input_file input type (fq/fa) [required]
reads raw/corrected reads [required]
sequencing_platform pacbio-raw pacbio-corrected nanopore-raw nanopore-
corrected [required]

optional arguments:
-h, --help show this help message and exit
-a [ASSEMBLER [ASSEMBLER ...]]
Chr-by_Chr assembler (canu flye miniasm) [default
canu]
-b Alignment block length [default 5000]
-p Alignment identity percentage [default 70%]
-l lowest number of misassemblies indecator [default 1]
-c Shortest contig length [default 5000]
-k Mis-assembly block [default 175]
It is better to extend the misassembly block in case of
unpolished assemblies or expected mis-assemblies
in highly repetative regions (5000-10000)
-q Mapping quality [default 20]
-f Output files name [default gathering]
-t cut on a threshold passed by -u [default False]
-u threshold cut value [default 3]
-o output files path [default current directory]
-v, --version show program's version number and exit

@zhaotao1987
Copy link
Author

Okay, I've saw this. ##4

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant