1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
|
RResolver
===================
RResolver, which stands for repeat or read resolver, whichever you prefer, improves genome assemblies at unitig stage by using a sliding window at read size level across repeats to determine which paths are correct.
Synopsis
===================
`abyss-rresolver-short " [OPTION]... <contigs> <graph> [<reads1> <reads2> ...]`
Options
===================
* `b`: read Bloom filter size. Unit suffixes 'K' (kilobytes), 'M' (megabytes), or 'G' (gigabytes) may be used. [`required`]
* `k`: assembly k-mer size [`required`]
* `g`: write the contig adjacency graph to FILE. [`required`]
* `c`: write the contigs to FILE [`required`]
* `j`: use N parallel threads [`1`]
* `h`: write the algorithm histograms with the given prefix. Histograms are omitted if no prefix is given.
* `t`: set path support threshold to N. [`4`]
* `x`: extract N r-mers per read. [`4`]
* `m`: set minimum number of sliding window moves to N. Cannot be higher than 127. [`20`]
* `M`: set maximum number of sliding window moves to N. Cannot be higher than 127. [`36`]
* `n`: set maximum number of branching paths to N. [`75`]
* `r`: explicitly set r value (k value used by rresolver). The number of set r values should be equal to the number of read sizes.
* `a`: explicitly set coverage approximation factor.
* `e`: enable correction of a 1bp error in kmers. [`false`]
* `S`: write supported paths to FILE.
* `U`: write unsupported paths to FILE.
Authors
===================
+ [**Vladimir Nikolic**](https://github.com/vlad0x00)
+ Supervised by [**Dr. Inanc Birol**](https://www.bcgsc.ca/people/inanc-birol).
Copyright 2021 Canada's Michael Smith Genome Sciences Centre
|
