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comparison configs/PacBio-CCS-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 PacBio CCS 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
9 # To use this configuration file, specify Shasta option "--config PathToThisFile".
10 # If you specify any conflicting values on the command line,
11 # the values specified on the command line take precedence.
12
13 # In most cases, for best performance on a large assembly
14 # you will usually also want to use the following options, which
15 # cannot be specified in a configuration file:
16 # --memoryMode filesystem
17 # --memoryBacking 2M
18 # Using these options require root access.
19
20 # For detailed information on all available options see here:
21 # https://chanzuckerberg.github.io/shasta/CommandLineOptions.html
22
23 # For information on running a small assembly for which
24 # performance is not essential see here:
25 # https://chanzuckerberg.github.io/shasta/QuickStart.html
26
27 # For more information on running an assembly see here:
28 # https://chanzuckerberg.github.io/shasta/Running.html
29
30 # For information on optimizing assembly performance see here:
31 # https://chanzuckerberg.github.io/shasta/Performance.html
32
33 [Kmers]
34 k = 15
35 probability = 0.02
36
37 [MinHash]
38 m = 12
39 minBucketSize = 20
40 maxBucketSize = 100
41 minHashIterationCount = 25
42 minFrequency = 10
43
44 [ReadGraph]
45 maxAlignmentCount = 20
46
47 [Assembly]
48 consensusCaller = Modal
49
50