Process Illumina instrument data into SAM/BAM/CRAM files.
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Updated
Jun 11, 2024 - C
Process Illumina instrument data into SAM/BAM/CRAM files.
Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
NGS4ECOPROD - An easy-to-use conda environment and pipelines for metagenome sequence analysis
RNA-seq pipeline for raw sequence alignment and transcript/gene quantification.
Aligns short reads using dynamic seed size with strobemers
SPAdes Genome Assembler
Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling
A pipeline to detect chimeric transcripts derived from genes and transposable elements.
A pipeline for determining the genomic location and transformation rules for the variants described in Illumina or Affymetrix genotype panel manifest files.
CheckQC inspects the content of an Illumina runfolder and determines if it passes a set of quality criteria
A quick and user-friendly pipeline to go from raw fastq data from Illumina (paired-end sequencing) to processed ASVs and Taxonomic data.
A state-of-the-art snakemake workflow for amplicon sequencing
UPHL's Reference Free Pipeline
Mapping-based Genome Size Estimation (MGSE) performs an estimation of a genome size based on a read mapping to an existing genome sequence assembly.
Public repo for the recount Bioconductor workflow that is visible at http://bioconductor.org/help/workflows/
R package for the recount2 project. Documentation website: http://leekgroup.github.io/recount/
Evaluating Nanopore-based bacterial variant calling
ClairS-TO - a deep-learning method for tumor-only somatic variant calling
A fully integrated K-mer Informed Toolkit for Bioinformatics
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