9 Software
BiocMAP makes use of several external software tools. The pipeline additionally supports the use of these tools via docker containers- this section also documents the docker images used in this mode.
9.1 Software Versions
Here is the full list of software used by this pipeline:
| Software | Version | Command used by the pipeline |
|---|---|---|
| Arioc | 1.43 | AriocE, AriocP, AriocU |
| Bismark | 0.23.0 | bismark_prepare_genome, bismark_methylation_extractor, bismark2bedgraph, coverage2cytosine |
| cmake | latest | cmake |
| fastQC | 0.11.8 | fastqc |
| htslib | 1.12 | (software library) |
| libBigWig | 0.4.6 | (software library) |
| java | 8+ | java |
| kallisto | 0.46.1 | kallisto |
| MethylDackel | 0.5.2 | MethylDackel extract |
| nextflow | >=0.27.0 (tested with 20.01.0) | nextflow |
| R | user-dependent | Rscript |
| samblaster | v.0.1.26 | samblaster |
| samtools | 1.10 | samtools |
| Trim Galore! | 0.6.6 | trim_galore |
9.2 Docker Images
The following image versions are used in this pipeline, when it is installed via the “docker” or “singularity” modes. These are automatically managed by BiocMAP.
| Image | Tag | Software |
|---|---|---|
| libddocker/arioc | 1.43 | Arioc |
| libddocker/bioc_kallisto | 3.17 | R 4.3.0, Bioconductor 3.17, Kallisto 0.46.1 |
| libddocker/bismark | 0.23.0 | Bismark |
| libddocker/filter_alignments | 1.0 | samtools 1.10, samblaster v.0.1.26 |
| libddocker/kallisto | 0.46.1 | Kallisto |
| libddocker/methyldackel | 0.5.2 | MethylDackel, samtools 1.10 |
| libddocker/quality_and_trim | 0.6.6 | FastQC 0.11.8, Cutadapt (latest), Trim Galore 0.6.6 |
| libddocker/ubuntu16.04_base | 1_v3 | Ubuntu Base |