Trending repositories for language Nextflow
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
Assembly and intrahost/low-frequency variant calling for viral samples
Single-cell RNA-Seq pipeline for barcode-based protocols such as 10x, DropSeq or SmartSeq, offering a variety of aligners and empty-droplet detection
Assembly and intrahost/low-frequency variant calling for viral samples
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
Single-cell RNA-Seq pipeline for barcode-based protocols such as 10x, DropSeq or SmartSeq, offering a variety of aligners and empty-droplet detection
Repository to host tool-specific module files for the Nextflow DSL2 community!
Assembly and intrahost/low-frequency variant calling for viral samples
Single-cell RNA-Seq pipeline for barcode-based protocols such as 10x, DropSeq or SmartSeq, offering a variety of aligners and empty-droplet detection
Assembly and intrahost/low-frequency variant calling for viral samples
A fully reproducible and state-of-the-art ancient DNA analysis pipeline
Repository to host tool-specific module files for the Nextflow DSL2 community!
Single-cell RNA-Seq pipeline for barcode-based protocols such as 10x, DropSeq or SmartSeq, offering a variety of aligners and empty-droplet detection
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
Eukaryotic Genome Annotation Pipeline-External caller scripts and documentation
Repository to host tool-specific module files for the Nextflow DSL2 community!
Single-cell/nuclei pipeline for data derived from Oxford Nanopore and 10X Genomics
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
Single-cell RNA-Seq pipeline for barcode-based protocols such as 10x, DropSeq or SmartSeq, offering a variety of aligners and empty-droplet detection
An analysis pipeline for long-reads from both PacBio and Oxford Nanopore Technologies (ONT), written in Nextflow.
(Meta-)genome screening for functional and natural product gene sequences
Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel
nextNEOpi: a comprehensive pipeline for computational neoantigen prediction
Single-cell/nuclei pipeline for data derived from Oxford Nanopore and 10X Genomics
An analysis pipeline for long-reads from both PacBio and Oxford Nanopore Technologies (ONT), written in Nextflow.
Eukaryotic Genome Annotation Pipeline-External caller scripts and documentation
(Meta-)genome screening for functional and natural product gene sequences
A pipeline for the analysis of CRISPR edited data. It allows the evaluation of the quality of gene editing experiments using targeted next generation sequencing (NGS) data (`targeted`) as well as the ...
nextNEOpi: a comprehensive pipeline for computational neoantigen prediction
Nextflow pipeline to analyze PacBio HiFi full-length 16S data
Pipeline to evaluate and validate the accuracy of variant calling methods in genomic research
Stochastic Testing and Input Manipulation for Unbiased Learning Systems
A pipeline to simulate sequencing reads, such as Amplicon, Target Capture, Metagenome, and Whole genome data.
Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq
A single cell transcriptomics pipeline for QC, integration and making the data presentable
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
Eukaryotic Genome Annotation Pipeline-External caller scripts and documentation
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
Repository to host tool-specific module files for the Nextflow DSL2 community!
Single-cell RNA-Seq pipeline for barcode-based protocols such as 10x, DropSeq or SmartSeq, offering a variety of aligners and empty-droplet detection
A single cell transcriptomics pipeline for QC, integration and making the data presentable
Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
Renders a collection of sequences into a pangenome graph. https://doi.org/10.1093/bioinformatics/btae609.
Eukaryotic Genome Annotation Pipeline-External caller scripts and documentation
Pipeline to evaluate and validate the accuracy of variant calling methods in genomic research
An analysis pipeline for long-reads from both PacBio and Oxford Nanopore Technologies (ONT), written in Nextflow.
Stochastic Testing and Input Manipulation for Unbiased Learning Systems
A Nextflow pipeline for evaluating assembly quality
A pipeline to run and systematically evaluate Multiple Sequence Alignment (MSA) methods.
Quantitative mass spectrometry workflow. Currently supports proteomics experiments with complex experimental designs for DDA-LFQ, DDA-Isobaric and DIA-LFQ quantification.
A pipeline for the analysis of CRISPR edited data. It allows the evaluation of the quality of gene editing experiments using targeted next generation sequencing (NGS) data (`targeted`) as well as the ...
Renders a collection of sequences into a pangenome graph. https://doi.org/10.1093/bioinformatics/btae609.
A nextflow pipeline for decontamination of short reads, long reads and contigs
Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq
Genome annotation with PacBio Iso-Seq. Takes raw subreads as input, generate Full Length Non Chemiric (FLNC) sequences and produce a bed annotation.
A pipeline to simulate sequencing reads, such as Amplicon, Target Capture, Metagenome, and Whole genome data.
AMR++ is a bioinformatic pipeline meant to aid in the analysis of raw sequencing reads to characterize the profile of antimicrobial resistance genes, or resistome.
rnasplice is a bioinformatics pipeline for RNA-seq alternative splicing analysis