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comparison configs/Nanopore-Dec2019.conf @ 0:60573349e9ae draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74"
author iuc
date Wed, 11 Nov 2020 21:54:51 +0000
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1 # This file contains Shasta options that, as of December 2019,
2 # are known to work with Oxford Nanopore reads under the following
3 # circumstances:
4
5 # - Human genome assembly.
6 # - Coverage between 40x and 80x. If you have more coverage than that,
7 # you can use option "--Reads.minReadLength" to adjust coverage as desired.
8 # - Reads from Guppy 3.0.5 base caller. Also known to work with
9 # reads from other Guppy releases 3.0.x and 3.1.x.
10
11 # To use this configuration file, specify Shasta option "--config PathToThisFile".
12 # If you specify any conflicting values on the command line,
13 # the values specified on the command line take precedence.
14
15 # In most cases, for best performance on a large assembly
16 # you will usually also want to use the following options, which
17 # cannot be specified in a configuration file:
18 # --memoryMode filesystem
19 # --memoryBacking 2M
20 # Using these options require root access.
21
22 # For detailed information on all available options see here:
23 # https://chanzuckerberg.github.io/shasta/CommandLineOptions.html
24
25 # For information on running a small assembly for which
26 # performance is not essential see here:
27 # https://chanzuckerberg.github.io/shasta/QuickStart.html
28
29 # For more information on running an assembly see here:
30 # https://chanzuckerberg.github.io/shasta/Running.html
31
32 # For information on optimizing assembly performance see here:
33 # https://chanzuckerberg.github.io/shasta/Performance.html
34
35
36
37 [Reads]
38 # If you have extra coverage, use this option to adjust coverage.
39 minReadLength = 10000
40
41 [MinHash]
42 minBucketSize = 5
43 maxBucketSize = 30
44 minFrequency = 5
45
46 [Align]
47 minAlignedFraction = 0.4
48
49 [Assembly]
50 consensusCaller = Bayesian:guppy-3.0.5-a
51