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# Miscellaneous things to process high throughput sequencing data. # Miscellaneous things to process high throughput sequencing data.
This Python package also installs a shell script depending on samtools: This Python package also installs some shell scripts:
`sam2indexedbam.sh`
* `sam2indexedbam.sh` (depends on samtools)
* `bam2bigwig.sh` (depends on bedops, python3, samtools, bedtools, niceload from parallel and bedGraphToBigWig from UCSC-tools)
## Installing ## Installing
...@@ -11,3 +14,9 @@ It might also work directly: ...@@ -11,3 +14,9 @@ It might also work directly:
python3 -m pip install git+ssh://git@gitlab.pasteur.fr/bli/libhts.git python3 -m pip install git+ssh://git@gitlab.pasteur.fr/bli/libhts.git
## Citing
If you use this package, please cite the following paper:
> Barucci et al, 2020 (doi: [10.1038/s41556-020-0462-7](https://doi.org/10.1038/s41556-020-0462-7))
...@@ -37,7 +37,7 @@ ...@@ -37,7 +37,7 @@
load_tools () load_tools ()
{ {
[ bedops --version 2> /dev/null ] || module load bedops/2.4.36 [ bedops --version 2> /dev/null ] || module load bedops/2.4.36
[ python3 -V 2> /dev/null ] || module load bedops/2.4.36 [ python3 -V 2> /dev/null ] || module load Python/3.7.2
[ samtools --version 2> /dev/null ] || module load samtools/1.9 [ samtools --version 2> /dev/null ] || module load samtools/1.9
[ bedtools --version 2> /dev/null ] || module load bedtools/2.25.0 [ bedtools --version 2> /dev/null ] || module load bedtools/2.25.0
[ niceload --version 2> /dev/null ] || module load parallel/20170122 [ niceload --version 2> /dev/null ] || module load parallel/20170122
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