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Source: yanosim
Section: science
Priority: optional
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Nilesh Patra <npatra974@gmail.com>
Build-Depends: debhelper-compat (= 13),
python3,
dh-python,
python3-setuptools,
# make sure python3-pysam is avaliable on all architectures to enable testing migration
python3-pysam
Standards-Version: 4.5.0
Vcs-Browser: https://salsa.debian.org/med-team/yanosim
Vcs-Git: https://salsa.debian.org/med-team/yanosim.git
Homepage: https://github.com/bartongroup/yanosim
Rules-Requires-Root: no
Testsuite: autopkgtest-pkg-python
Package: yanosim
Architecture: any
Depends: ${shlibs:Depends},
${misc:Depends},
${python3:Depends},
python3-numpy,
python3-scipy,
python3-click,
python3-pysam
Description: read simulator nanopore DRS datasets
Yanosim has three options:
.
1. yanosim model:
Creates an model of mismatches, insertions and deletions
based on an alignment of nanopore DRS reads to a
reference. Reads should be aligned to a transcriptome
i.e. without spliced alignment, using minimap2. They
should have the cs tag.
2. yanosim quantify:
Quantify the number of reads mapping to each
transcript in a reference, so that the right number
of reads can be simulated.
3. yanosim simulate:
Given a model created using yanosim model, and
per-transcript read counts created using yanosim
simulate, simulate error-prone long-reads from the
given fasta file.
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