pinfish
Collection of tools to annotate genomes using long read transcriptomics data
Command lineScience
Not tested on a device yet. What that means
Commands in the package
cluster_gffcollapse_partialspolish_clustersspliced_bam2gff
About pinfish
From Debian's package description
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.
From Debian's description of the pinfish package, under that package's license.
Dependencies
Depends on
Related apps
- dcGNU dc arbitrary precision reverse-polish calculatorCommand line
- spatialite-binGeospatial extension for SQLite - toolsCommand line
ASE GUIAtomic Simulation Environment GUI- trimmomaticflexible read trimming tool for Illumina NGS dataCommand line
- minimap2versatile pairwise aligner for genomic and spliced nucleotide sequencesCommand line
- sim4dbbatch spliced alignment of cDNA sequences to a target genomeCommand line
Sources and licenses
- Name: the Debian package name.
- Summary: Debian's short description of the pinfish package, under that package's license.
- Description: Debian's description of the pinfish package, under that package's license.
- Versions and sizes: Debian's archive for ARM64, as on packages.debian.org.
- Popularity: Debian Popularity Contest counts.
More in About the catalog.