add Rasusa for subsampling ONT reads

close #13

README.md

@@ -9,7 +9,7 @@ See the preprint here: [Snakemake Workflows for Long-read Bacterial Genome Assem
 
 | read filtering | assembly | long read polishing | short read polishing | reference-based polishing |
 | --- | --- | --- | --- | --- |
-| [Filtlong](https://github.com/rrwick/Filtlong) | [Flye](https://github.com/fenderglass/Flye)<br/> [raven](https://github.com/lbcb-sci/raven)<br/> [miniasm](https://github.com/lh3/miniasm)<br/> [Unicycler](https://github.com/rrwick/Unicycler)<br/> [Canu](https://github.com/marbl/canu)  | [racon](https://github.com/lbcb-sci/racon)<br/> [medaka](https://github.com/nanoporetech/medaka) | [pilon](https://github.com/broadinstitute/pilon/wiki)<br/> [Polypolish](https://github.com/rrwick/Polypolish)<br/> [POLCA](https://github.com/alekseyzimin/masurca#polca) | [Homopolish](https://github.com/ythuang0522/homopolish)<br/> [proovframe](https://github.com/thackl/proovframe) | 
+| [Filtlong](https://github.com/rrwick/Filtlong)<br/> [Rasusa](https://github.com/mbhall88/rasusa) | [Flye](https://github.com/fenderglass/Flye)<br/> [raven](https://github.com/lbcb-sci/raven)<br/> [miniasm](https://github.com/lh3/miniasm)<br/> [Unicycler](https://github.com/rrwick/Unicycler)<br/> [Canu](https://github.com/marbl/canu)  | [racon](https://github.com/lbcb-sci/racon)<br/> [medaka](https://github.com/nanoporetech/medaka) | [pilon](https://github.com/broadinstitute/pilon/wiki)<br/> [Polypolish](https://github.com/rrwick/Polypolish)<br/> [POLCA](https://github.com/alekseyzimin/masurca#polca) | [Homopolish](https://github.com/ythuang0522/homopolish)<br/> [proovframe](https://github.com/thackl/proovframe) | 
 
 
 ## Quick start
@@ -114,6 +114,17 @@ The output is written to `fastq-ont/mysample+filtlongMB<m>,<q>,<l>,<n>.fastq`.
 
 When using any of the Filtlong keywords in a folder name, they must be followed by an underscore, followed by the keyword for the assembler.
 
+### Rasusa
+The ONT reads can be randomly subsampled prior to the assembly.
+
+The available keywords are:
+
+**`rasusaMB<m>`**  
+This will subsample the ONT reads to a total of `m` megabases.  
+The output is written to `fastq-ont/mysample+rasusaMB<m>.fastq`.
+
+When using any the Rasusa keyword in a folder name, it must be followed by an underscore, followed by the keyword for the assembler.
+
 ### Flye
 
 Following keywords can be used to run the assembly with Flye:

Snakefile

@@ -43,11 +43,13 @@ wildcard_constraints:
 def get_ont_fq(wildcards):
     if "filtlong" in wildcards.sample:
         return "fastq-ont/" + wildcards.sample + ".fastq"
+    elif "rasusa" in wildcards.sample:
+        return "fastq-ont/" + wildcards.sample + ".fastq"
     else:
         return glob("fastq-ont/" + wildcards.sample + ".fastq*")
 
 
-# use split("+")[0] here for removing the +filtlong... suffices from sample names for Illumina reads
+# use split("+")[0] here for removing the +filtlong... or +rasusa... suffices from sample names for Illumina reads
 def get_R1_fq(wildcards):
     return glob("fastq-illumina/" + wildcards.sample.split("+")[0] + "_R1.fastq*")
 
@@ -161,6 +163,21 @@ rule filtlong:
         """
 
 
+rule rasusaMB:
+    conda:
+        "env/conda-rasusa.yaml"
+    threads: 1
+    input:
+        fq=get_ont_fq,
+    output:
+        "fastq-ont/{sample}+rasusaMB{num}.fastq",
+    log:
+        "fastq-ont/{sample}_rasusaMB{num}_log.txt",
+    shell:
+        """
+         rasusa --bases {wildcards.num}m -i {input} -o {output} 2>{log}
+        """
+
 rule filtlongMB:
     threads: 1
     input:

env/conda-rasusa.yaml

@@ -0,0 +1,9 @@
+name: ont-assembly-snake-rasusa
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+  - anaconda
+dependencies:
+  - bioconda::rasusa=0.7.1
+