All Published Workflows
17 workflows that have been reviewed and published
Snakemake pipeline for de novo transcriptome assembly with 454 reads
This is a workflow to assemble RNA reads from 454 into a transcriptome. The procedure is as follows:
Quality control
...
Annotating Novel lncRNAs Using Existing Annotations: A Snakemake-Based Pipeline
A Snakemake-based pipeline to annotate novel lncRNA using existing annotation. This pipeline uses various bioinformatics tool...
circDetector (CD): circular RNAs detection and annotation workflow
circDetector (CD) is a computational tool for detecting and annotation of circular RNAs (circRNAs) from Total RNA-Seq data...
circDetector (CD): Circular RNA Detection and Annotation Workflow
circDetector (CD) is a computational tool for detecting and annotation of circular RNAs (circRNAs) from Total RNA-Seq data...
The repository host the snakemake file for 16S rRNA and shotgun sequencing data including QIIME2 and kraken2/bracken for 16S and metaphalan3 and kraken2/bracken for shotgun.
This is an ongoing project to generate a snakemake workflow to anlaysis 16S rRNA and shotgun seqeucnign microbial data using ...
RIC-seq-based Prediction of Complementary RNA-RNA Contacts
Prediction of complementary regions between RNA-RNA contacts derived from RIC-seq data. Developed by Sergei Margasyuk (smarga...
Transcriptomics Data Quality Control and Adapter Trimming Workflow
Implementation homework for transcriptomics As discribed in task:
performed fastqc
performed multiqc
trimmed barc...
Cleaning transcriptome annotations with ab initio assemblers
AnnotationCleaner is designed to automate the construction of ab initio assembled transcriptomes using several different tool...
Pipeline for RNA and DNA integrated analysis for somatic mutation detection
Hi beta-tester, thanks for agreeing to help out in this
repo. I have created a project to add issues/tasks.
Plese feel fr...
Analysis of long non-coding RNAs from RNA-seq datasets
A Nextflow-based pipeline for comprehensive analyses of long non-coding RNAs from RNA-seq datasets Recently, long noncodin...
gatk4 RNA variant calling pipeline
nf-core/rnavar is a bioinformatics best-practice analysis pipeline for GATK4 RNA variant calling. The pipeline is built us...
A small-RNA sequencing analysis pipeline
nf-core/smrnaseq is a bioinformatics best-practice analysis pipeline for Small RNA-Seq. The pipeline is built using Next...