TRON-Bioinformatics / covigator-ngs-pipelineLinks
A Nextflow pipeline for NGS variant calling on SARS-CoV-2. From FASTQ files to normalized and annotated VCF files from GATK, BCFtools, LoFreq and iVar.
☆19Updated last year
Alternatives and similar repositories for covigator-ngs-pipeline
Users that are interested in covigator-ngs-pipeline are comparing it to the libraries listed below
Sorting:
- Workflow to prepare high accuracy single molecule consensus sequences from amplicon data using unique molecular identifiers☆33Updated last year
- An R package for estimating poly(A)-tail lengths in Oxford Nanopore RNA and DNA reads.☆54Updated 9 months ago
- catalog for long-read sequencing tools☆32Updated 2 years ago
- modPhred is a pipeline for detection of DNA/RNA modifications from raw ONT data☆16Updated last year
- A tutorial on structural variant calling for short read sequencing data☆39Updated 8 months ago
- Freddie: Annotation-independent detection and discovery of transcriptomic alternative splicing isoforms using long-read sequencing☆16Updated 2 years ago
- ☆51Updated 5 years ago
- WDL workflows for variant calling and assembly using ONT☆35Updated last month
- Methylation Phasing for Nanopore Sequencing☆48Updated 2 years ago
- new repo☆28Updated 4 years ago
- Filter SAM file for soft and hard clipped alignments☆49Updated last year
- A snakemake pipeline for SV analysis from nanopore genome sequencing☆51Updated 5 years ago
- Simple utility to concatenate .fastq(.gz) files whilst creating a summary of the sequences.☆42Updated 2 weeks ago
- SAMStat displays various properties of next-generation sequencing reads stored in SAM/BAM format.☆24Updated last year
- My collection of light bioinformatics analysis pipelines for specific tasks☆75Updated last year
- Fully automated generation of UCSC assembly hubs☆34Updated 9 months ago
- ☆31Updated 2 years ago
- Master of Pores 2☆23Updated 7 months ago
- LongcallR is a SNP caller for single molecule long-read RNA-seq data☆62Updated 2 weeks ago
- NANOME pipeline (Nanopore long-read sequencing consensus DNA methylation detection method and pipeline)☆31Updated last week
- Tools to annotate genomes using long read transcriptomics data☆46Updated 4 years ago
- perSVade: personalized Structural Variation detection☆40Updated last week
- PhyloCSF++ computes PhyloCSF tracks for whole-genome multiple sequence alignments, scores single MSA, annotates CDS features in GFF/GTF f…☆31Updated 3 years ago
- Long-read splice alignment with high accuracy☆63Updated 9 months ago
- Error correction of ONT transcript reads☆58Updated last year
- curPrimers is a tool for trimming primer sequences from amplicon based NGS reads☆16Updated last month
- A python tool box for fast and accurate quality control, conversion and alignment of nanopore sequencing data☆20Updated 3 years ago
- TIDDIT - structural variant calling☆74Updated 3 months ago
- Dot: An interactive dot plot viewer for comparative genomics☆33Updated 2 years ago
- Pipeline for de novo clustering of long transcriptomic reads☆26Updated 3 years ago