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77class Plasmids (Recipe ):
88 """
9-
9+ Plasmid detection pipeline using mapping, mash_screen and assembly with
10+ SPAdes, with gene annotations with abricate. Outputs json files that
11+ can be imported into pATLAS.
1012 """
1113
1214 def __init__ (self ):
@@ -23,7 +25,8 @@ def __init__(self):
2325
2426class PlasmidsMapping (Recipe ):
2527 """
26-
28+ Plasmid detection pipeline using mapping with bowtie2. Outputs json
29+ files that can be imported into pATLAS.
2730 """
2831
2932 def __init__ (self ):
@@ -38,7 +41,8 @@ def __init__(self):
3841
3942class PlasmidsAssembly (Recipe ):
4043 """
41-
44+ Plasmid detection pipeline using assembly with SPAdes and mash dist.
45+ Outputs json files that can be imported into pATLAS.
4246 """
4347
4448 def __init__ (self ):
@@ -55,7 +59,8 @@ def __init__(self):
5559
5660class PlasmidsMash (Recipe ):
5761 """
58-
62+ Plasmid detection pipeline using mash screen. Outputs json files that can
63+ be imported into pATLAS.
5964 """
6065
6166 def __init__ (self ):
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