pinfish 0.1.0+ds-2 source package in Ubuntu
Changelog
pinfish (0.1.0+ds-2) unstable; urgency=medium * Limit testing to amd64 and arm64 for now * Source-only-upload for testing migration -- Nilesh Patra <email address hidden> Tue, 10 Nov 2020 14:51:27 +0530
Upload details
- Uploaded by:
- Debian Med
- Uploaded to:
- Sid
- Original maintainer:
- Debian Med
- Architectures:
- any all
- Section:
- misc
- Urgency:
- Medium Urgency
See full publishing history Publishing
| Series | Published | Component | Section |
|---|
Downloads
| File | Size | SHA-256 Checksum |
|---|---|---|
| pinfish_0.1.0+ds-2.dsc | 2.5 KiB | e525e50cbbabf276e0daf1bfb4165f8f78396cda75265b906026eac3d2ae9123 |
| pinfish_0.1.0+ds.orig-debian-tests-data.tar.xz | 65.4 MiB | 40957e398ab9bebdc89fe69dbef1c816da544e69a6aeed9c04371430f61f53bb |
| pinfish_0.1.0+ds.orig.tar.xz | 4.8 MiB | c8213acc3f88d9e1294b9f9014a28b8fd410ebe0aab4793c7bb7263e7e465e4d |
| pinfish_0.1.0+ds-2.debian.tar.xz | 6.3 KiB | 2f51b7af7ce10ad7418aa3ae177caf69b67636427f1b5c689b5f480bb8268168 |
Available diffs
- diff from 0.1.0+ds-1 to 0.1.0+ds-2 (439 bytes)
No changes file available.
Binary packages built by this source
- pinfish: Collection of tools to annotate genomes using long read transcriptomics data
The toolchain is composed of the following tools:
1. spliced_bam2gff - a tool for converting sorted BAM
files containing spliced alignments
into GFF2 format. Each read will be represented as a distinct
transcript. This tool comes handy when visualizing spliced
reads at particular loci and to provide input to the rest
of the toolchain.
.
2. cluster_gff - this tool takes a sorted GFF2 file as
input and clusters together reads having similar
exon/intron structure and creates a rough consensus
of the clusters by taking the median of exon
boundaries from all transcripts in the cluster.
.
3. polish_clusters - this tool takes the cluster
definitions generated by cluster_gff and for each
cluster creates an error corrected read by mapping
all reads on the read with the median length
and polishing it using racon. The polished reads
can be mapped to the genome using minimap2 or GMAP.
.
4. collapse_partials - this tool takes GFFs generated
by either cluster_gff or polish_clusters and filters
out transcripts which are likely to be based on RNA
degradation products from the 5' end. The tool clusters
the input transcripts into "loci" by the 3' ends and
discards transcripts which have a compatible transcripts
in the loci with more exons.
- pinfish-dbgsym: debug symbols for pinfish
- pinfish-examples: Examples and test data for pinfish
The toolchain is composed of the following tools:
1. spliced_bam2gff - a tool for converting sorted BAM
files containing spliced alignments
into GFF2 format. Each read will be represented as a distinct
transcript. This tool comes handy when visualizing spliced
reads at particular loci and to provide input to the rest
of the toolchain.
.
2. cluster_gff - this tool takes a sorted GFF2 file as
input and clusters together reads having similar
exon/intron structure and creates a rough consensus
of the clusters by taking the median of exon
boundaries from all transcripts in the cluster.
.
3. polish_clusters - this tool takes the cluster
definitions generated by cluster_gff and for each
cluster creates an error corrected read by mapping
all reads on the read with the median length
and polishing it using racon. The polished reads
can be mapped to the genome using minimap2 or GMAP.
.
4. collapse_partials - this tool takes GFFs generated
by either cluster_gff or polish_clusters and filters
out transcripts which are likely to be based on RNA
degradation products from the 5' end. The tool clusters
the input transcripts into "loci" by the 3' ends and
discards transcripts which have a compatible transcripts
in the loci with more exons.
.
This package contains a test data set as well as sample scripts
running some test suite provided by Debian also as autopkgtest.
