hivdb / codfreqLinks
FASTQ-to-CodFreq pipeline for HIV-1 and SARS-CoV-2
☆14Updated last year
Alternatives and similar repositories for codfreq
Users that are interested in codfreq are comparing it to the libraries listed below
Sorting:
- ☆24Updated 3 months ago
- Protein Alignment and Detection Interface☆61Updated last year
- Reference-guided multiple sequence alignment of viral genomes☆70Updated 2 months ago
- Design degenerated primers on highly variable alignments for full genome sequencing or qPCR. Specifically developed for viruses.☆41Updated 2 months ago
- A pipeline for preprocessing NGS data from Illumina, Nanopore and PacBio technologies☆34Updated last year
- Ultra-efficient taxonomic mapping of NGS data☆52Updated 4 years ago
- A program for degenerate primer design for broad taxonomic-range PCR for microbial ecology studies☆30Updated 2 years ago
- Multilocus sequence typing by blast using the schemes from PubMLST☆30Updated 3 years ago
- SAMStat displays various properties of next-generation sequencing reads stored in SAM/BAM format.☆24Updated 2 years ago
- Code for design of diagnostic PCR primers, and metabarcoding markers.☆62Updated last year
- The Zika bioinformatics pipeline☆35Updated 5 years ago
- A nextflow pipeline for decontamination of short reads, long reads and contigs☆50Updated last month
- OPAL: Open-community Profiling Assessment tooL☆30Updated 6 months ago
- My collection of light bioinformatics analysis pipelines for specific tasks☆75Updated last year
- Automatically design multiplex PCR primer pairs for diverse templates☆29Updated last year
- This repository houses the code to run SURPI+, a rapid computational pipeline for comprehensive identification of pathogens from clinical…☆41Updated 5 years ago
- Mutation tracker for microbial genomes☆15Updated 4 years ago
- A pipeline for high-quality bacterial genome construction using ONT sequencing☆39Updated 2 years ago
- ShortBRED is a pipeline to take a set of protein sequences, reduce them to a set of unique identifying strings ("markers"), and then sear…☆31Updated 6 months ago
- ☆27Updated 5 years ago
- MIRA sequence assembler☆29Updated 7 months ago
- ☆28Updated 3 years ago
- ThermoAlign: software for automated primer design☆27Updated 7 years ago
- Workflow to prepare high accuracy single molecule consensus sequences from amplicon data using unique molecular identifiers☆33Updated last year
- Python bindings for the TaxonKit library☆41Updated last month
- VIRULIGN: fast codon-correct alignment and annotation of viral genomes☆35Updated 4 years ago
- 🍶 Genome assembly with short sequence reads☆25Updated last year
- Influenza genome analysis Nextflow workflow☆28Updated last week
- This is the codebase for Recycler, described in our manuscript: https://academic.oup.com/bioinformatics/article/33/4/475/2623362, by Roye…☆59Updated 4 years ago
- Flash2 has some improvements from flash_1 including new logic from innie and outie overlaps as well as some initial steps for flash for a…☆50Updated 7 years ago