actc

Align clr to ccs reads.

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What is this about?

If you want to have one-click solution to align subreads to the respective CCS reads.

How to install

Use bioconda

conda install -c bioconda actc

Download binary directly

Get binary from releases and make it executable.

Compile manually

mkdir build && cd build
meson --prefix ~/mytools
ninja
ninja install

How to run

actc movie.subreads.bam movie.ccs.bam aligned.bam --log-level INFO

Output files

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.

Pre-conditions

• The CCS file must be a subset of the ZMWs of the subread input file.
• The CLR file must be indexed, a subreads.bam.pbi can be generated via pbindex
• The CLR file must be sorted by ZMW, default for subreads.bam

Chunking

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>

How to index BAM files

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

Changelog

• 0.6.0
  • Add --trim-flanks-bp to clip N bases from each flank
  • Add --min-ccs-length, trimmed CCS reads shorter than N bp are ignored
• 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 @PG to BAM header
  • Auto generate version from meson.build
  • Improve (de)compression, ergo throughput, by threading
• 0.0.3
  • Use subreads read groups
  • Fix FASTA output for --chunk
  • Initial attempt to increase throughput
• 0.0.2
  • Add --chunk capabilities
• 0.0.1
  • Intial release