A quick and user-friendly pipeline to go from raw fastq data from Illumina (paired-end sequencing) to processed ASVs and Taxonomic data.
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Updated
May 30, 2024 - R
A quick and user-friendly pipeline to go from raw fastq data from Illumina (paired-end sequencing) to processed ASVs and Taxonomic data.
Workflow and R scripts for Giongo et al. (2024)
A modernized ART for Illumina read simulation.
Generate a .CSV manifest file for importing multiple samples in the Illumina MiSeq machine
Automated pipeline for amplicon sequence analysis
VIral GEnome ASsembly pipelines for WGS
genome assembler for cleaning, mapping and assembling genomes.
code getter for illumina, pacbio, oxford long reads alignments.
A collection of publications on comparison of high-throughput sequencing technologies.
🚀 A sequencing simulator
Detection of Saccharomyces paradoxus DNA across Saccharomyces cerevisiae, and vice versa.
Parse Illumina InterOp folder
RNA-Seq Pipeline for processing paired-end FASTQ transcripts generated from Illumina sequencing. The pipeline trims adapter sequences, aligns transcripts to a specified region of interest on the reference genome, and facilitates downstream analysis.
Create fastq symlinks for selected samples in sequencer output directories based on several criteria
Accompanying information to a scientific publication on the assembly of bacterial genomes using Illumina and nanopore sequencing data using Unicylcer.
ABBA-BABA test conducted on Saccharomyces cerevisiae strains using whole-genome alignment.
Generate simulated illumina sequence reads from a reference sequence
A pipeline for variant calling from P. falciparum short reads generated from Illumina and ONT libraries
Scripts supporting the manuscript submitted to the Molecular Ecology Resources Special Issue 'Omics for species conservation'
C++ Library to parse Illumina InterOp files
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