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Viral Annotation DefineR: classification and annotation of viral sequences based on RefSeq annotation
NCBI Datasets is a new resource that lets you easily gather data from across NCBI databases.
Salmonella serotyping from genome sequencing data
NGS-PrimerPlex is a high-throughput tool for mupltiplex primer design
SISTR (Salmonella In Silico Typing Resource) command-line tool
An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes
Official code repository for GATK versions 4 and up
A bioinformatics software tool for clinical interpretation of genetic variants by the 2015 ACMG-AMP guideline
Annotation of VCF variants with functional impact and from databases (executable+library)
multiPrime is a mismatch-tolerant minimal primer set design tool for large and diverse sequences (e.g. Virus). Here is a web-based version (test: http://multiPrime.cn))
Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement
HoCoRT - Remove specific organisms from sequencing reads
Automatically exported from code.google.com/p/cdhit
An ultrafast memory-efficient short read aligner
🎨 Visualisation toolbox for beautiful and publication-ready figures
Quality control tool on metagenomic and metatranscriptomic sequencing data, especially data from microbiome experiments.
The second version of the Kraken taxonomic sequence classification system
An illumina paired-end and mate-pair short read simulator. This project attempts to model as many of the quirks that exist in Illumina data as possible. Some of these quirks include the potential f…
Cutadapt removes adapter sequences from sequencing reads
Primer3 is a command line tool to select primers for polymerase chain reaction (PCR).
The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants