nebiolabs / ampseer
Ampseer examines reads in fastq format and identifies which multiplex PCR primer set was used to generate the SARS-CoV-2 sequencing library they are read from. It is intended to differentiate between ARTIC v3, ARTIC v4, ARTIC v4.1, VarSkip 1a, VarSkip 2, Midnight and VarSkip Long primer sets sequenced by Illumina or ONT.
☆14Updated 8 months ago
Related projects ⓘ
Alternatives and complementary repositories for ampseer
- Automated Pipeline to Generate FTP Files and Manage Submission of Sequence Data to Public Repositories☆32Updated this week
- ☆15Updated this week
- Fast viral consensus genome reconstruction☆22Updated 4 months ago
- Whole genome core alignments from multiple draft genomes☆12Updated 8 years ago
- Read contamination removal☆24Updated 9 months ago
- TaxTriage is a Nextflow workflow designed to agnostically identify and classify microbial organisms within short- or long-read metagenomi…☆23Updated this week
- NCBI Pathogen Detection Portal toolkit☆11Updated last year
- TAXnomic Profile Aggregation and STAndardisation☆34Updated last week
- Remove contaminated contigs from genomes using k-mers and taxonomies.☆53Updated last year
- Strip reads from Oxford Nanopore FAST5 files if they meet certain criteria☆14Updated 3 years ago
- Experiments with using BIGSI data structure for metagenomic and QC applications☆18Updated 2 months ago
- Get microbial sequence data easier and faster☆28Updated 5 years ago
- a tool to filter sites in a FASTA-format whole-genome pseudo-alignment☆37Updated last month
- Output FASTQ summary statistics in JSON format☆29Updated 2 years ago
- Build a map of genes present across a set of microbial genomes☆12Updated last month
- A mathematically characterized hypothesis test for organism presence/absence in a metagenome☆30Updated this week
- CFSAN Shigella Typing Pipeline☆14Updated last year
- in silico typing of the H. influenzae cap locus☆11Updated 3 months ago
- Evaluating Nanopore-based bacterial variant calling☆14Updated last month
- Colinear block visualisation tool☆30Updated 9 months ago
- UPHL's Reference Free Pipeline☆25Updated this week
- Fast and space-efficient taxonomic classification of long reads☆42Updated last week
- Phylogenetic maximum representation sampling: choosing most representative strains or taxa☆29Updated 3 weeks ago
- Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)☆22Updated last month
- List and download schemes from pubMLST.org and other BIGSDB servers☆8Updated 3 weeks ago
- Plasmid analysis using rearrangement distances☆29Updated 2 months ago
- Recombination-free trees☆56Updated last year
- Snakemake workflow for scoring and comparing multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s).☆24Updated 7 months ago
- Intra-species bacterial contamination detection☆22Updated last year