14 open source projects by tseemann

✂️ ⚡️ Rapid haploid variant calling and core genome alignment

🔎 💊 Mass screening of contigs for antimicrobial and virulence genes

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

🔬 ♌️ Bacterial ribosomal RNA predictor

🆔 Scan contig files against PubMLST typing schemes

Pairwise SNP distance matrix from a FASTA sequence alignment

🔬🐛 Rapid 16s rRNA identification from isolate FASTQ files

⚡️ ♒️ Rapid prokaryotic genome annotation

Convert various sequence formats to FASTA

Assembly based core genome SNP alignments for bacteria

Identify phage regions in bacterial genomes for masking purposes

📈 Automatically optimise three of Velvet's assembly parameters.

💾 📃 "Reads to report" for public health and clinical microbiology

🍊 💫 Trim, circularise and orient long read bacterial genome assemblies