Align clr to ccs reads.
If you want to have one-click solution to align subreads to the respective CCS reads.
conda install -c bioconda actc
Get binary from releases and make it executable.
mkdir build && cd build
meson --prefix ~/mytools
ninja
ninja install
actc movie.subreads.bam movie.ccs.bam aligned.bam --log-level INFO
Main output file aligned.bam contains all alignments,
in the same order as they occur in the inputs.
Auxilliary file aligned.fasta contains all references of the alignment file.
- The CCS file must be a subset of the ZMWs of the subread input file.
- The CLR file must be indexed, a
subreads.bam.pbican be generated viapbindex - The CLR file must be sorted by ZMW, default for
subreads.bam
You can parallelize by chunking, via --chunk is possible. For this, the
ccs.bam file must accompanied by a .pbi file.
An example workflow, all actc invocations can run simultaneously:
actc movie.subreads.bam movie.ccs.bam aligned.1.bam --chunk 1/10 -j <THREADS>
actc movie.subreads.bam movie.ccs.bam aligned.2.bam --chunk 2/10 -j <THREADS>
...
actc movie.subreads.bam movie.ccs.bam aligned.10.bam --chunk 10/10 -j <THREADS>
To generate the BAM index
.bam.pbi, use pbindex, which can be installed with conda install pbbam.
pbindex movie.ccs.bam
pbindex movie.subreads.bam
- 0.6.0
- Add
--trim-flanks-bpto clip N bases from each flank - Add
--min-ccs-length, trimmed CCS reads shorter than N bp are ignored
- Add
- 0.5.0
- Allow unsorted uBAM CCS input
- 0.4.0
- Accept REVIO files
- 0.3.0
- Properly handle flanks
- 0.2.0
- Improve runtime and reduce memory footprint for low-complexity molecules
- 0.1.0
- Add actc
@PGto BAM header - Auto generate version from
meson.build - Improve (de)compression, ergo throughput, by threading
- Add actc
- 0.0.3
- Use subreads read groups
- Fix FASTA output for
--chunk - Initial attempt to increase throughput
- 0.0.2
- Add
--chunkcapabilities
- Add
- 0.0.1
- Intial release
