Nextflow Modules
Showing module(s) with keyword "transcriptome"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| nf-core/bam_dedup_umi | Workflow | deduplication UMI BAM genome transcriptome umicollapse umitools | BAM deduplication with UMI processing for both genome and transcriptome alignments |
| nf-core/busco/busco | Process | quality control genome transcriptome proteome | Benchmarking Universal Single Copy Orthologs |
| nf-core/busco/download | Process | quality control genome transcriptome proteome | Download database for BUSCO |
| nf-core/busco/generateplot | Process | genome fasta annotation busco transcriptome quality control | BUSCO plot generation tool |
| nf-core/busco/plot | Process | genome fasta annotation busco transcriptome quality control | BUSCO summary plot generation using the built-in 'busco --plot' command |
| nf-core/gstama/collapse | Process | tama_collapse.py isoseq nanopore long-read transcriptome gene model TAMA | Collapse redundant transcript models in Iso-Seq data. |
| nf-core/mudskipper/bulk | Process | bam transcriptome transcriptomic mudskipper sam rad | Convert genomic BAM/SAM files to transcriptomic BAM/RAD files. |
| nf-core/mudskipper/index | Process | bam transcriptome transcriptomic index mudskipper sam | Build and store a gtf index, which is useful for converting genomic BAM/SAM files to transcriptomic BAM/SAM files. |
| nf-core/simpleaf/index | Process | indexing transcriptome gene expression SimpleAF | Indexing of transcriptome for gene expression quantification using SimpleAF |
| nf-core/transrate | Process | transcriptome assembly quality control qc de novo | Reference-free and reference-based quality assessment of de novo transcriptome assemblies. Only sequence-based (--assembly) and reference-based (--reference) metrics are supported. Read-based metrics (--left/--right) are not: they hard-require the `bam-read` binary, which isn't published on any conda channel, and their aligner (snap-aligner, pinned to an old dev build) segfaults building an index for at least small test genomes. |