⚡ ♒ Rapid prokaryotic genome annotation

Trinity RNA-Seq de novo transcriptome assembly

Automatically exported from code.google.com/p/cdhit

✂️ ⚡ Rapid haploid variant calling and core genome alignment

The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants

🔎 💊 Mass screening of contigs for antimicrobial and virulence genes

Extensive de-novo TE Annotator

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.

🔬 ♌ Microbial RNA annotation

RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.

TransDecoder source

🆔 Scan contig files against PubMLST typing schemes

⚡♠️ Assemble bacterial isolate genomes from Illumina paired-end reads

STAR-Fusion codebase

De-Novo Repeat Discovery Tool

A scalable high-throughput metabolic and biogeochemical functional trait profiler

Any Way to Show Multi genomic Synteny

LDBlockShow: a fast and convenient tool for visualizing linkage disequilibrium and haplotype blocks based on VCF files

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.

Genome Assembly and Annotation Service code

PASA software

VarDict

🌳 Create a tree using Mash distances

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

🐉 🪰 Assemble bacterial isolate genomes from Nanopore reads