lskatz / SneakerNetLinks
QA/QC pipeline for a MiSeq/HiSeq/Ion Torrent/assembly-only run
☆11Updated 10 months ago
Alternatives and similar repositories for SneakerNet
Users that are interested in SneakerNet are comparing it to the libraries listed below
Sorting:
- INNUENDO quality control of reads, de novo assembly and contigs quality assessment, and possible contamination search☆15Updated 2 years ago
- Read contamination removal☆25Updated last year
- Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)☆28Updated 3 months ago
- Predict MLST directly from uncorrected long reads☆27Updated 3 years ago
- Assembly based core genome SNP alignments for bacteria☆25Updated 6 years ago
- Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes☆15Updated 7 years ago
- Interactive, web tool for exploring pan-genome of bacterial strains☆48Updated 2 years ago
- ☆14Updated 4 years ago
- pipeline for read mapping, snp calling and annotation for bacterial genomes☆13Updated last year
- Mycobacterium tuberculosis genomic analysis from Nanopore sequencing data☆12Updated last year
- Colinear block visualisation tool☆31Updated last year
- CFSAN Shigella Typing Pipeline☆15Updated 2 years ago
- Strip reads from Oxford Nanopore FAST5 files if they meet certain criteria☆14Updated 4 years ago
- Sequence-independent identification and removal of adapters/systemic contamination in shotgun sequencing data. https://doi.org/10.1093/bi…☆17Updated 2 years ago
- Output FASTQ summary statistics in JSON format☆29Updated 2 years ago
- Intra-species bacterial contamination detection☆25Updated 8 months ago
- Snakemake workflow for scoring and comparing multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s).☆26Updated last year
- Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database☆42Updated 4 years ago
- Get microbial sequence data easier and faster☆28Updated 5 years ago
- UPHL's Reference Free Pipeline☆27Updated 3 weeks ago
- frame-shift correction for long-read (meta)genomics☆33Updated last year
- Automated Pipeline to Generate FTP Files and Manage Submission of Sequence Data to Public Repositories☆38Updated 2 weeks ago
- Genomic neighbor typing of bacterial pathogens using MinHash☆43Updated 2 years ago
- Fast and space-efficient taxonomic classification of long reads☆43Updated 2 months ago
- 🍊 💫 Trim, circularise and orient long read bacterial genome assemblies☆25Updated 6 years ago
- software to identify primers that can distinguish genomes☆20Updated 9 months ago
- Cluster informed Shigella and EIEC serotyping tool from Illumina reads and assemblies☆12Updated 2 years ago
- Strain-level haplotyping for metagenomes with short or long-reads.☆55Updated 6 months ago
- Genome size estimation from long read overlaps☆62Updated last month
- Remove human reads from a sequencing run☆40Updated 2 months ago