Raven
Raven is a de novo genome assembler for long uncorrected reads.
Using in SGE_Batch
Make sure you are in bash, and generate a shell script with your commands that
you want to submit over SGE. Add the source /local/cluster/raven/activate.sh
line before your commands to access the programs over SGE.
To activate:
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bash
source /local/cluster/raven/activate.sh
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Location and version:
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$ which raven
/local/cluster/raven/bin/raven
$ raven --version
1.7.0
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help message:
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usage: raven [options ...] <sequences> [<sequences> ...]
# default output is to stdout in FASTA format
<sequences>
input file in FASTA/FASTQ format (can be compressed with gzip)
options:
-k, --kmer-len <int>
default: 15
length of minimizers used to find overlaps
-w, --window-len <int>
default: 5
length of sliding window from which minimizers are sampled
-f, --frequency <double>
default: 0.001
threshold for ignoring most frequent minimizers
-p, --polishing-rounds <int>
default: 2
number of times racon is invoked
-m, --match <int>
default: 3
score for matching bases
-n, --mismatch <int>
default: -5
score for mismatching bases
-g, --gap <int>
default: -4
gap penalty (must be negative)
--graphical-fragment-assembly <string>
prints the assembly graph in GFA format
--resume
resume previous run from last checkpoint
--disable-checkpoints
disable checkpoint file creation
-t, --threads <int>
default: 1
number of threads
--version
prints the version number
-h, --help
prints the usage
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software ref: https://github.com/lbcb-sci/raven
research ref: https://doi.org/10.1038/s43588-021-00073-4