Trycycler
Trycycler is a tool for generating consensus long-read assemblies for
bacterial genomes. I.e. if you have multiple long-read assemblies for the same
isolate, Trycycler can combine them into a single assembly that is better than
any of your inputs.
For installation instructions, usage, deeper explanations and more, head over
to the Trycycler wiki!
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/trycycler/activate.sh line before your commands to access
the programs over SGE.
To activate:
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bash
source /local/cluster/trycycler/activate.sh
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Location and version:
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$ which trycycler
/local/cluster/trycycler/bin/trycycler
$ trycycler --version
Trycycler v0.5.3
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help message:
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$ trycycler --help
usage: trycycler [-h] [--version]
{subsample,cluster,dotplot,reconcile,msa,partition,consensus}
...
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Trycycler: a consensus long-read assembly tool
Commands:
{subsample,cluster,dotplot,reconcile,msa,partition,consensus}
subsample: subsample a long-read set
cluster: cluster contigs by similarity
dotplot: draw pairwise dotplots for a cluster
reconcile: reconcile contig sequences
msa: multiple sequence alignment
partition: partition reads by cluster
consensus: derive a consensus sequence
Help:
-h, --help Show this help message and exit
--version Show program's version number and exit
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software ref: https://github.com/rrwick/Trycycler
software ref: https://github.com/rrwick/Trycycler/wiki
research ref: https://doi.org/10.1186/s13059-021-02483-z