chanzuckerberg / czid-dag
Please see https://github.com/chanzuckerberg/czid-workflows for the latest version of CZ ID workflows.
☆27Updated 3 years ago
Alternatives and similar repositories for czid-dag:
Users that are interested in czid-dag are comparing it to the libraries listed below
- Assembler for raw de novo genome assembly of long uncorrected reads.☆37Updated 5 years ago
- A method of assessing sequence complexity based on kmer frequencies☆32Updated 7 years ago
- Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI☆29Updated 6 years ago
- de novo virus assembler of Illumina paired reads☆55Updated 3 years ago
- Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database☆41Updated 4 years ago
- Antibiotic resistance predictions in minutes on a laptop☆50Updated 6 years ago
- variant discovery and annotation using GATK and Ensembl☆17Updated 11 years ago
- Metagenomic profiling and phylogenetic distances via common kmers☆42Updated 3 years ago
- ☆23Updated 5 years ago
- Find Unique genomic Regions☆29Updated 3 weeks ago
- Ococo: the first online variant and consensus caller. Call genomic consensus directly from an unsorted SAM/BAM stream.☆47Updated 6 years ago
- Collection of utilities for working with PacBio-based assemblies☆13Updated 2 years ago
- full taxonomer cython repository☆22Updated 5 years ago
- Homebrew formulae for bioinformatics software only available for Linux☆27Updated 5 years ago
- Workflows I find helpful for fungal genome annotation☆21Updated last year
- PARTIE is a program to partition sequence read archive (SRA) metagenomics data into amplicon and shotgun data sets. The user-supplied ann…☆25Updated 2 years ago
- Error correction for Oxford Nanopore data☆47Updated 3 years ago
- Output FASTQ summary statistics in JSON format☆29Updated 2 years ago
- A draft genome scaffolder that uses multiple reference genomes in a graph-based approach.☆44Updated 4 years ago
- Scripts for creating a Kraken database from the Comprehensive Antibiotic Resistance Database☆10Updated 8 years ago
- Public Health England SNP calling pipeline.☆36Updated 6 years ago
- The Zika bioinformatics pipeline☆36Updated 5 years ago
- DEPRECIATED! Please use nf-core/tools instead☆19Updated 6 years ago
- Amplicon Sequencing Analysis Pipeline☆16Updated last week
- De novo Extraction of Strains from MetAgeNomes☆68Updated 4 years ago
- ☆25Updated 8 years ago
- ☆14Updated 6 years ago
- k-SLAM ultra fast alignment and taxonomic classification of metagenomic datasets☆23Updated 6 years ago
- 🍶 Genome assembly with short sequence reads☆25Updated last year
- MicrobeDirectory 2.0☆22Updated 4 years ago