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A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data
The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants
🔎 💊 Mass screening of contigs for antimicrobial and virulence genes
BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET/EP/ETP and AUGUSTUS in novel eukaryotic genomes
Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms
A collection of sequencing protocols and bioinformatic resources for SARS-CoV-2 sequencing.
GALBA is a pipeline for fully automated prediction of protein coding gene structures with AUGUSTUS in novel eukaryotic genomes for the scenario where high quality proteins from one or several close…
Biopieces is a bioinformatic framework of tools easily used and easily created.
💾 📃 "Reads to report" for public health and clinical microbiology
GET_HOMOLOGUES: a versatile software package for pan-genome analysis
Learning the Sequence Alignment/Map format
Robust detection of clinically relevant structural and copy number variation from whole genome sequencing data
RetroSeq is a bioinformatics tool that searches for mobile element insertions from aligned reads in a BAM file and a library of reference transposable elements. Please read the wiki page (link belo…
phenotype-based prioritization of candidate genes for human diseases
Amplicon sequencing pipelines suitable for SSU (16S, 18S), LSU (23S, 28S) and ITS.
Mutation Identification Pipeline. Read the latest documentation:
MTBseq is an automated pipeline for mapping, variant calling and detection of resistance mediating and phylogenetic variants from illumina whole genome sequence data of Mycobacterium tuberculosis c…
Identify phage regions in bacterial genomes for masking purposes
Website for Computational Exome and Genome Analysis
GARFIELD-NGS: Genomic vARiants FIltering by dEep Learning moDels in NGS
The Exome Coverage and Identification Report displays the coverage of every target region in your capture design. It also displays regions below an adjustable coverage threshold.
MeGAMerge (A tool to merge assembled contigs, long reads from metagenomic sequencing runs)
🐾 QA/QC pipeline for a MiSeq/HiSeq/Ion Torrent/assembly-only run