PiGx: Pipelines in Genomics

[Steffen Möller <steffen_moeller@gmx.de>]

Hello,

I was just pointed to PIGx (https://bioinformatics.mdc-berlin.de/pigx/ ,
https://doi.org/10.1093/gigascience/giy123 ) that offers several
pipelines for "next generation" sequencing:

  *

    PiGx BSseq <https://github.com/BIMSBbioinfo/pigx_bsseq> for raw
    fastq read data of bisulfite experiments

  *

    PiGx RNAseq <https://github.com/BIMSBbioinfo/pigx_rnaseq> for RNAseq
    samples

  *

    PiGx scRNAseq <https://github.com/BIMSBbioinfo/pigx_scrnaseq> for
    single cell dropseq analysis

  *

    PiGx ChIPseq <https://github.com/BIMSBbioinfo/pigx_chipseq> for
    reads from ChIPseq experiments

  *

    PiGx CRISPR <https://github.com/BIMSBbioinfo/pigx_crispr> /(work in
    progress)/ for the analysis of sequence mutations in CRISPR-CAS9
    targeted amplicon sequencing data

It ships with test scripts and data. Their package management is with
GUIX. Anyway, this could be something for us to get some "we can
workflow"-stamp before we have bcbio done. I looked at
https://github.com/BIMSBbioinfo/pigx_rnaseq/blob/master/requirements.txt and
https://github.com/BIMSBbioinfo/pigx_scrnaseq/blob/master/requirements.txt
which does not look too bad. I have just packaged a few dependencies for
it that we did not have with us, yet (trim_galore, the CRAN packages
corrplot (very nice, did not know about that one) and gProfiler (long
overdue)), and now I am a bit stuck on the BioConductor package
tximport, see separate email. But it very much seems like we are getting
there very quickly.

Best,

Steffen