-
Notifications
You must be signed in to change notification settings - Fork 2
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
- Loading branch information
Showing
2 changed files
with
639 additions
and
2 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -1,2 +1,77 @@ | ||
# wtdbg2-racon-pilon.pl | ||
Wrapper for overlap assembly of long reads and polishing | ||
# wtdbg2-racon-pilon.pl v0.3 | ||
|
||
## Description | ||
__Automatic execution of (wtdbg2,) racon and pilon.__ | ||
|
||
Longread assembly will be executed with wtdbg2. | ||
Iterative correction with long reads by mapping to the assembly with minimap2 and polishing with Racon. | ||
Iterative correction with short reads by mapping with either bwa mem or NextGenMap, (merging and) sorting of bam files with samtools and polishing with Pilon. | ||
|
||
## Dependencies | ||
|
||
`wtdbg2-racon-pilon.pl` will search for the following executables in your `$PATH`: | ||
|
||
__Assembly__ | ||
- [wtdbg2](https://github.com/ruanjue/wtdbg2): `wtdbg2`, `wtpoa-cns` | ||
|
||
__Long read polishing__ | ||
- [Racon](https://github.com/isovic/racon): `racon` | ||
- [Minimap2](https://github.com/lh3/minimap2): `minimap2` | ||
|
||
__Short read polishing__ | ||
- Java: `java` | ||
- [bwa (mem)](https://github.com/lh3/bwa): `bwa` | ||
- [NextGenMap](http://cibiv.github.io/NextGenMap/): `ngm` | ||
- [samtools](https://github.com/samtools/samtools): `samtools` | ||
- [Pilon](https://github.com/broadinstitute/pilon): Specify the path to Pilon `jar` file with `-pilon-path` | ||
|
||
## Usage | ||
|
||
``` | ||
wtdbg2-racon-pilon.pl {-l <longreads.fq> -x <longread tech> | -a <assembly.fa>} | ||
[-p <paired_1.fq>,<paired_2.fq> -u <unpaired.fq>] | ||
Mandatory: | ||
-l STR File containing long reads in fastq format | ||
-x STR Long read sequencing technology for wtdbg2 presets | ||
Valid arguments are: rsII, rs, sequel, sq, nanopore, ont, | ||
corrected, ccs | ||
OR | ||
-a STR File containing an assembly that should be polished in fasta format | ||
Input/pipeline options: [default] | ||
-racon-rounds INT Number of racon iterations [3] | ||
-pilon-rounds INT Number of pilon iterations [3] | ||
-pilon-path STR Complete path to the pilon jar file | ||
-sr-mapper STR Short read mapper for correction with pilon [bwa] | ||
Valid arguments are: bwa, ngm | ||
To execute different mappers in different pilon rounds supply a | ||
comma separated list of mappers. Overrides -pilon-rounds. | ||
-p STR Two files with paired short reads in fastq format comma sperated | ||
Can be specified multiple times | ||
-u STR One file with unpaired short reads in fastq format | ||
Can be specified multiple times | ||
-xmx STR/INT Maximum java heap size for pilon [current available] | ||
-t INT Number of parallel executed processes [1] | ||
Affects wtdbg2, wtpoa-cns, minimap2, racon, bwa mem, ngm, | ||
samtools sort and pilon. | ||
Pass specific options to tools with: | ||
-wtdbg-opts, -wtpoa-opts, -minimap-opts, -racon-opts, -bwa-opts, -ngm-opts, -pilon-opts | ||
For example like -wtdbg-opts '-g 100m' | ||
Output options: [default] | ||
-o STR Output directory [.] | ||
Will be created if not existing | ||
-pre STR Prefix of output files [{w|<-a>.}r<racon rounds>p<pilon rounds>] | ||
-v Print executed commands to STDERR [off] | ||
-dry-run Only print commands to STDERR instead of executing [off] | ||
-h or -help Print this help and exit | ||
-version Print version number and exit | ||
``` | ||
|
||
## Citation | ||
If you use this tool please cite the dependencies. | ||
|
||
## Known issues | ||
In some cases Pilon can not polish the assembly with bam files created by NextGenMap. |
Oops, something went wrong.