nanopolish | Signal-level algorithms for MinION data | Genomics library
kandi X-RAY | nanopolish Summary
kandi X-RAY | nanopolish Summary
Software package for signal-level analysis of Oxford Nanopore sequencing data. Nanopolish can calculate an improved consensus sequence for a draft genome assembly, detect base modifications, call SNPs and indels with respect to a reference genome and more (see Nanopolish modules, below).
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nanopolish Examples and Code Snippets
Community Discussions
Trending Discussions on nanopolish
QUESTION
I am writing a snakemake pipeline to eventually identify corona virus variants.
Below is a minimal example with three steps:
...ANSWER
Answered 2021-Jun-10 at 07:54I think the problem is that rule catFasta
doesn't contain the wildcard barcode
. If you think about it, what job name would you expect in {wildcards.barcode}.{rule}.{jobid}
?
Maybe a solution could be to add to each rule a jobname
parameter that could be {barcode}
for guppyplex
and minion
and 'all_barcodes'
for catFasta
. Then use --jobname "{params.jobname}.{rule}.{jobid}"
QUESTION
I am writing a snakemake to produce Sars-Cov-2 variants from Nanopore sequencing. The pipeline that I am writing is based on the artic network, so I am using artic guppyplex
and artic minion
.
The snakemake that I wrote has the following steps:
- zip all the
fastq
files for all barcodes (rulezipFq
) - perform read filtering with
guppyplex
(ruleguppyplex
) - call the
artic minion
pipeline (ruleminion
) - move the stderr and stdout from qsub to a folder under the working directory (rule
mvQsubLogs
)
Below is the snakemake that I wrote so far, which works
...ANSWER
Answered 2021-Jun-08 at 15:40The rule that fails is rule guppyplex
, which looks for an input in the form of {FASTQ_PATH}/{{barcode}}
.
Looks like the wildcard {barcode}
is filled with barcode49/barcode49.consensus.fasta
, which happened because of two reasons I think:
First (and most important): The workflow does not find a better way to produce the final output. In rule catFasta
, you give an input file which is never described as an output in your workflow. The rule minion
has the directory as an output, but not the file, and it is not perfectly clear for the workflow where to produce this input file.
It therefore infers that the {barcode}
wildcard somehow has to contain this .consensus.fasta
that it has never seen before. This wildcard is then handed over to the top, where the workflow crashes since it cannot find a matching input file.
Second: This initialisation of the wildcard with sth. you don't want is only possible since you did not constrain the wildcard properly. You can for example forbid the wildcard to contain a .
(see wildcard_constraints
here)
However, the main problem is that catFasta
does not find the desired input. I'd suggest changing the output of minion
to "nanopolish/{barcode}/{barcode}.consensus.fasta"
, since the you already take the OUTDIR from the params, that should not hurt your rule here.
Edit: Dummy test example:
QUESTION
So I have an issue when I run other programs after I ran flye in my snakemake pipeline. This is because the output from flye is a directory. My rules are as followd:
...ANSWER
Answered 2019-Nov-11 at 21:08(I think) The problem lies somewhere else in your code.
You have defined two rules, the first that outputs directory assembled
, the second that outputs assembled/assembly.fasta
. Since the output of the second rule is always at least the directory assembled
, Snakemake complains. You can solve it by using the directory as input:
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