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Trinity RNA-Seq de novo transcriptome assembly
Automatically exported from code.google.com/p/cdhit
✂️ ⚡ Rapid haploid variant calling and core genome alignment
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
Rapid large-scale prokaryote pan genome analysis
A collection of sequencing protocols and bioinformatic resources for SARS-CoV-2 sequencing.
RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.
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A scalable high-throughput metabolic and biogeochemical functional trait profiler
LTR_retriever is a highly accurate and sensitive program for identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also included in this package.
LDBlockShow: a fast and convenient tool for visualizing linkage disequilibrium and haplotype blocks based on VCF files
ALLHiC: phasing and scaffolding polyploid genomes based on Hi-C data
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…
💾 📃 "Reads to report" for public health and clinical microbiology