biology/atac-seq - The NetBSD Packages Collection

Core tools needed for ATAC-Seq analysis

The atac-seq meta-package provides the core tools needed for performing
a typical ATAC-Seq differential accessibility analysis, including
adapter trimming, quality control, alignment, peak calling, and
identification of differentially accessible peaks.  Researchers may
want additional tools for data manipulation, gene ontology, etc.

Build dependencies

pkgtools/mktools pkgtools/cwrappers

Runtime dependencies

biology/fastq-trim biology/fastqc biology/biolibc-tools biology/gffread biology/bwa biology/bowtie2 biology/samtools biology/igv biology/py-macs2 biology/fasda biology/peak-classifier biology/py-multiqc www/webbrowser www/curl lang/python311 lang/python311

Binary packages

NetBSD 10.0_BETAx86_64atac-seq-1.2.1nb1.tgz
NetBSD 8.0x86_64atac-seq-1.2.1nb1.tgz
NetBSD 8.0x86_64atac-seq-1.1.tgz
NetBSD 8.0x86_64atac-seq-1.1.tgz
NetBSD 9.0x86_64atac-seq-1.2.1nb1.tgz
NetBSD 9.0x86_64atac-seq-1.1.tgz
NetBSD 9.0x86_64atac-seq-1.1.tgz
NetBSD 9.3x86_64atac-seq-1.2.1.tgz
NetBSD 9.3x86_64atac-seq-1.1.tgz

Binary packages can be installed with the high-level tool pkgin (which can be installed with pkg_add) or pkg_add(1) (installed by default). The NetBSD packages collection is also designed to permit easy installation from source.

Available build options


Known vulnerabilities

The pkg_admin audit command locates any installed package which has been mentioned in security advisories as having vulnerabilities.

Please note the vulnerabilities database might not be fully accurate, and not every bug is exploitable with every configuration.

Problem reports, updates or suggestions for this package should be reported with send-pr.