Package Recipe 'pysam'

recipe pysam¶

Pysam is a python module for reading and manipulating Samfiles. It is a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix.

Homepage:	https://github.com/pysam-developers/pysam
License:	MIT
Recipe:	/pysam/meta.yaml
Links:	biotools: pysam, doi: 10.1093/bioinformatics/btp352

package pysam¶

(downloads)

Versions:	0.15.2-2, 0.15.2-1, 0.15.2-0, 0.15.1-0, 0.15.0.1-1, 0.15.0.1-0, 0.15.0-0, 0.14.1-1, 0.14.1-0, 0.14.0-2, 0.14.0-1, 0.14.0-0, 0.13.0-0, 0.12.0.1-2, 0.12.0.1-1, 0.12.0.1-0, 0.11.2.2-2, 0.11.2.2-1, 0.11.2.2-0, 0.11.2.1-0, 0.11.1-0, 0.11.0-0, 0.10.0-8, 0.10.0-7, 0.10.0-6, 0.10.0-5, 0.10.0-4, 0.10.0-3, 0.10.0-1, 0.9.1.4-1, 0.9.1.4-0, 0.9.1-6, 0.9.1-5, 0.9.1-4, 0.9.1-3, 0.9.1-2, 0.9.1-1, 0.9.1-0, 0.9.0-2, 0.9.0-1, 0.9.0-0, 0.8.4-0, 0.8.4pre0-0, 0.8.3-6, 0.8.3-5, 0.8.3-4, 0.8.3-3, 0.8.3-2, 0.8.3-1, 0.8.3-0, 0.7.7-3, 0.7.7-2, 0.7.7-1, 0.7.7-0
Depends:	bcftools 1.9.* curl >=7.64.0,<8.0a0 htslib >=1.9,<1.10.0a0 libdeflate >=1.0,<1.1.0a0 python >=2.7,<2.8.0a0 samtools 1.9.* zlib >=1.2.11,<1.3.0a0
Required By:	targqc rnftools kipoi_veff rgt qcat svtyper pbalign genomelake whatshap cgat-daisy dkfz-bias-filter monovar uropa quasitools riboplot gretel compare-reads pydnase sqt gimmemotifs mockinbird afplot riboseq-rust plastid metaphlan2 biofluff tetoolkit strainest circexplorer2 moca mvp wub metaseq ariba seqcluster nucleoatac deeptools daisysuite pbcoretools dupre scanindel mirtop pepr rpkmforgenes python-bioext reparation_blast rmats2sashimiplot cnvkit peakachu crossmap relocate2 ribocode mgkit desman advntr prophyle imfusion pomoxis cpat tophat-recondition pbcore circlator bioconvert gemini athena_meta guidescan svim umitools bcbio-nextgen optitype counterr cgat-scripts mapdamage2 lumpy-sv midas sequana riboraptor transposcope htseq refinem riboseed vcfpy outrigger cooler anvio-minimal mqc atropos smallgenomeutilities hifive flaimapper pygenometracks genomicassertions wisecondorx svviz segmentation-fold phenix phyluce nanosv oncotator edd emirge discasm cgat-apps probamconvert umis nanoget checkm-genome clinvar-tsv sixgill pysamstats pyloh tepid wg-blimp icount confindr metasv pyseer ebfilter pneumocat fast5seek nanoplot nanosim bs-seeker2 breakseq2 smcounter2 rseqc dr-disco spanki vqsr_cnn ribotish xyalign recycler umi_tools misopy circexplorer iclipro slamdunk iva epic2 medaka somaticseq ctat-mutations atactk pybedtools besst connor samsift hicexplorer blockclust simlord tigmint starseqr hap.py bcbio-nextgen-vm ngsutils comparative-annotation-toolkit rna-cd

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install pysam

and update with:

conda update pysam

or use the docker container:

docker pull quay.io/biocontainers/pysam:<tag>

(see pysam/tags for valid values for <tag>)

Link to this page¶

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