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 last year
Alternatives and similar repositories for ampseer:
Users that are interested in ampseer are comparing it to the libraries listed below
- Read contamination removal☆25Updated last year
- Whole genome core alignments from multiple draft genomes☆13Updated 8 years ago
- Strip reads from Oxford Nanopore FAST5 files if they meet certain criteria☆14Updated 3 years ago
- Remove contaminated contigs from genomes using k-mers and taxonomies.☆56Updated last year
- Experiments with using BIGSI data structure for metagenomic and QC applications☆19Updated 8 months ago
- Automated Pipeline to Generate FTP Files and Manage Submission of Sequence Data to Public Repositories☆38Updated 3 weeks ago
- Fast and space-efficient taxonomic classification of long reads☆43Updated 2 months ago
- NCBI Pathogen Detection Portal toolkit☆11Updated last year
- ☆21Updated 2 months ago
- CFSAN Shigella Typing Pipeline☆14Updated last year
- Output FASTQ summary statistics in JSON format☆30Updated 2 years ago
- Strain-level haplotyping for metagenomes with short or long-reads.☆51Updated 3 weeks ago
- Get microbial sequence data easier and faster☆28Updated 5 years ago
- Colinear block visualisation tool☆30Updated last year
- A method of assessing sequence complexity based on kmer frequencies☆32Updated 7 years ago
- software to identify primers that can distinguish genomes☆21Updated 3 months ago
- interactive barplot for amplicon sequencing☆14Updated 5 months ago
- A curated database of completed assemblies with taxonomy IDs☆44Updated 4 months ago
- Fast viral consensus genome reconstruction☆22Updated 4 months ago
- in silico typing of the H. influenzae cap locus☆12Updated 9 months ago
- Remove human reads from a sequencing run☆40Updated 7 months ago
- Minimizer-based assembly scaffolding and mapping using long reads☆39Updated 6 months ago
- TaxTriage is a Nextflow workflow designed to agnostically identify and classify microbial organisms within short- or long-read metagenomi…☆34Updated this week
- ☆30Updated last year
- Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database☆41Updated 4 years ago
- Automatic eukaryotic taxonomic classification☆28Updated 2 weeks ago
- Genome size estimation from long read overlaps☆55Updated 3 weeks ago
- SARs-CoV-2 Primer schemes☆15Updated 2 years ago
- Kraken2 Server☆21Updated last year
- REcombination BARcode detector.☆13Updated last year