Prepare reads with just --reads_name about baga HOT 2 CLOSED

Yes:

baga_cli.py PrepareReads --adaptors fullsample --reads_name <myreads>

The default option for --adaptors is actually subsample which uses the output --subsample_to_cov produces. The above command goes to the original read files given to CollectData. Some documentation for the different command line tasks is available via:

baga_cli.py PrepareReads -h

Similarly, if your reads are ready for analysis and you don't need any of the PrepareReads options you can skip it with --prepared in the alignment step, e.g.:

baga/baga_cli.py AlignReads \
--reads_name Liverpool \
--genome_name NC_011770.1 \
--prepared \
--align --deduplicate

Cheers! I hope it comes in useful.

Development is on going. One particular limitation worth knowing about is BAGA doesn't handle multi-replicon genomes i.e., one or more chromosomes and/or plasmids. But work is underway for that - let me know if you'd need that sooner than later.

from baga.

👍 Thanks for the quick reply and this is definitely something the lab will make use of. I am currently working with a multi-replicon genome (1 chr and 1 plasmid). However, I know there are no variants on the plasmid. Working through the data now on the AWS EC2. Thanks again. Also, fine to close if you'd like.

from baga.