shorah

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is shorah same as lofreq?

4

Hi all, does shorah algorithms follow the same principle as lofreq? thanks Ibseq

ibseq

Error running Amplicon with diversity option

3

## Shorah Version: 1.99.2 ## Command to reproduce: ``` $ shorah amplicon -b my_sorted_bam.bam -f amplicon.fasta -d ``` > I have trimmed my read length to equal length prior to...

XU-Nuo

# [Added] - Ports `b2w.cpp` to Python utilizing `pysam` - Replaces Travis with Github Actions - Introduces Sphinx for documentation # [Removed] - `b2w.cpp` # [Fixed] - `reads.fas` # Breaking...

spaceben

I installed shorah using conda. I successfully installed it on macOS. But when I am trying to run the example amplicon_test gives me an error saying command not found: smalt....

Ruchank1

Long reads - nanopore

5

Hello, I'm interested in using this tool, but before I go down the rabbit hole of installing this tool, I would like to know if it works with long read...

Psy-Fer

xref https://github.com/galaxyproject/tools-iuc/issues/3516 ``` Traceback (most recent call last): File "/dep/_conda/envs/[email protected]/lib/python3.6/logging/handlers.py", line 71, in emit if self.shouldRollover(record): File "/dep/_conda/envs/[email protected]/lib/python3.6/logging/handlers.py", line 187, in shouldRollover msg = "%s\n" % self.format(record) File "/dep/_conda/envs/[email protected]/lib/python3.6/logging/init.py", line...

bernt-matthias

Shorah: UnboundLocalError: local variable 'end' referenced before assignment

1

Hi, I am running shorah (installed with conda) and I am getting an error, my command line is: > shorah shotgun -b my_bam.bam -f CoV.fasta -a 0.1 -w 201 -x...

ptapiaisp

Conda package: no version file

4

See error report below: ``` (shorah) [dvoretsk@ouga03 REGION_1]$ shorah Traceback (most recent call last): File "/opt/modules/i12g/anaconda/envs/shorah/lib/python3.6/site-packages/shorah/cli.py", line 50, in __version__ = get_distribution('shorah').version File "/opt/modules/i12g/anaconda/envs/shorah/lib/python3.6/site-packages/pkg_resources/__init__.py", line 481, in get_distribution dist =...

stefanches7

ShoRAH: Illumina reads ; influenza

7

Dear, I am very interest in using your tool for my project. I'm working on influenza reads that were sequenced with Illumina MiSeq. I was able to extract quasispecies with...

LauraVP1994

Conda package for 1.99 not working properly

13

I tried to install shorah via bioconda (conda install -c biconda shorah) and executing shorah will give the following error: `pkg_resources.DistributionNotFound: The 'shorah' distribution was not found and is required...

heylf