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

Versions

0.15.2-3, 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 >=7.64.1,<8.0a0

• htslib >=1.9,<1.10.0a0

• libdeflate >=1.0,<1.1.0a0

• libgcc-ng >=7.3.0

• python >=2.7,<2.8.0a0

• samtools 1.9.*

• zlib >=1.2.11,<1.3.0a0

Required By

• somaticseq

• sequana

• riboseed

• desman

• advntr

• anvio-minimal

• circle-map

• pyloh

• ebfilter

• umitools

• wisecondorx

• epic2

• genomelake

• microhapulator

• gretel

• samsift

• fast5seek

• pb-falcon

• paragraph

• tepid

• biofluff

• crossmap

• quasitools

• probamconvert

• checkm-genome

• dkfz-bias-filter

• pbalign

• rnftools

• rpkmforgenes

• umis

• guidescan

• smcounter2

• outrigger

• besst

• mockinbird

• deeptools

• nanoget

• moca

• nanosv

• circexplorer2

• cgat-apps

• bcbio-nextgen-vm

• genomicassertions

• afplot

• kipoi_veff

• compare-reads

• discasm

• athena_meta

• edd

• cnvkit

• counterr

• ariba

• iclipro

• prophyle

• spanki

• sixgill

• dupre

• sqt

• comparative-annotation-toolkit

• gimmemotifs

• atropos

• htseq

• targqc

• peakachu

• telescope

• tigmint

• qcat

• confindr

• igv-reports

• trnanalysis

• mirtop

• clinvar-tsv

• connor

• strainest

• pomoxis

• hifive

• mark-nonconverted-reads

• metaphlan2

• phenix

• tophat-recondition

• atactk

• circexplorer

• relocate2

• icount

• lumpy-sv

• nanoplot

• starseqr

• pydnase

• pneumocat

• pybedtools

• hap.py

• pbcore

• svviz

• phyluce

• monovar

• wg-blimp

• ribotish

• optitype

• scanindel

• tetoolkit

• mapdamage2

• tiddit

• flaimapper

• transposcope

• samplot

• bcbio-nextgen

• whatshap

• refinem

• emirge

• ngsutils

• python-bioext

• ribotricer

• simlord

• bioconvert

• misopy

• cooler

• cpat

• rmats2sashimiplot

• midas

• tobias

• vcfpy

• daisysuite

• rna-cd

• ribocode

• iva

• hicexplorer

• pygenometracks

• wub

• pepr

• svim

• ctat-mutations

• metasv

• breakseq2

• pysamstats

• mgkit

• insilicoseq

• reparation_blast

• smallgenomeutilities

• plastid

• seqcluster

• dr-disco

• pbcoretools

• segmentation-fold

• xyalign

• pyseer

• blockclust

• rgt

• cgat-scripts

• mqc

• oncotator

• svtyper

• ipyrad

• tapestry

• mvp

• gemini

• medaka

• imfusion

• recycler

• circlator

• slamdunk

• guessmylt

• rseqc

• cgat-daisy

• riboplot

• sv2

• wisestork

• bs-seeker2

• umi_tools

• riboseq-rust

• uropa

• bamread

• nucleoatac

• vqsr_cnn

• nanosim

• riboraptor

• metaseq

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

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/pysam/README.html)