lskatz / SneakerNet
QA/QC pipeline for a MiSeq/HiSeq/Ion Torrent/assembly-only run
☆11Updated last month
Related projects ⓘ
Alternatives and complementary repositories for SneakerNet
- Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)☆22Updated last month
- Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes☆15Updated 6 years ago
- Read contamination removal☆24Updated 9 months ago
- INNUENDO quality control of reads, de novo assembly and contigs quality assessment, and possible contamination search☆13Updated last year
- A pipeline for bioinformatics analysis of bacterial genomes☆19Updated 4 months ago
- Intra-species bacterial contamination detection☆22Updated this week
- Visualisation application for Klebsiella genotypes generated by Kleborate.☆9Updated 3 years ago
- a tool to filter sites in a FASTA-format whole-genome pseudo-alignment☆37Updated this week
- Snakemake workflow for scoring and comparing multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s).☆24Updated 7 months ago
- pipeline for read mapping, snp calling and annotation for bacterial genomes☆11Updated 8 months ago
- CFSAN Shigella Typing Pipeline☆14Updated last year
- Assembly based core genome SNP alignments for bacteria☆25Updated 5 years ago
- Interactive, web tool for exploring pan-genome of bacterial strains☆45Updated last year
- 🍊 💫 Trim, circularise and orient long read bacterial genome assemblies☆25Updated 5 years ago
- Strip reads from Oxford Nanopore FAST5 files if they meet certain criteria☆14Updated 3 years ago
- Output FASTQ summary statistics in JSON format☆29Updated 2 years ago
- BACTpipe: An assembly and annotation pipeline for bacterial genomics☆20Updated 2 years ago
- Cluster informed Shigella and EIEC serotyping tool from Illumina reads and assemblies☆11Updated last year
- Standalone Python re-implementation of the POLCA polisher from MaSuRCA☆28Updated 2 months ago
- Code to create a PRG from a Multiple Sequence Alignment file☆22Updated 7 months ago
- UPHL's Reference Free Pipeline☆25Updated 2 weeks ago
- transposable element typing pipeline☆16Updated 8 months ago
- tool to determine optimal refrerence genome given a set of fasta files☆14Updated last year
- Formats Roary output for viewing in FriPan☆10Updated 6 years ago
- A script for comparing old vs new versions of genome annotations☆20Updated last year
- Mycobacterium tuberculosis genomic analysis from Nanopore sequencing data☆11Updated 5 months ago
- Predict MLST directly from uncorrected long reads☆25Updated 2 years ago
- A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data☆29Updated last month
- Strain-level haplotyping for metagenomes with short or long-reads.☆41Updated 4 months ago