ncbi / pipelinesLinks
☆13Updated 7 years ago
Alternatives and similar repositories for pipelines
Users that are interested in pipelines are comparing it to the libraries listed below
Sorting:
- PARTIE is a program to partition sequence read archive (SRA) metagenomics data into amplicon and shotgun data sets. The user-supplied ann…☆24Updated 2 years ago
- Antibiotic resistance predictions in minutes on a laptop☆50Updated 6 years ago
- de novo virus assembler of Illumina paired reads☆58Updated 4 years ago
- Protein Alignment and Detection Interface☆60Updated last year
- benchmarking and containerization of tools for analysis of complex non-clinical metagenomes.☆21Updated 7 years ago
- Interactive, web-based BLAST results visualization tool. Accessible at https://kablammo.wasmuthlab.org.☆67Updated 3 years ago
- Tutorial on using E-utilities☆23Updated 8 months ago
- Get, parse, and extract information from the SRA metadata files☆45Updated 3 years ago
- Extract lineage CSVs from NCBI for use with sourmash lca.☆29Updated 2 years ago
- The Zika bioinformatics pipeline☆36Updated 5 years ago
- Prepares a SARS-CoV-2 submission for GISAID, NCBI or ENA. Can read GISAID or NCBI files, or plain fasta+tsv/csv/xls. Finds files in input…☆36Updated 3 years ago
- Assembler for raw de novo genome assembly of long uncorrected reads.☆36Updated 5 years ago
- EMIRGE reconstructs full length ribosomal genes from short read sequencing data.☆37Updated 2 years ago
- This RAPT repository has been retired as of December 2024. NCBI's Read assembly and Annotation Pipeline Tool (RAPT) was a pilot service.☆58Updated 7 months ago
- A resistome profiler for Graphing Resistance Out Of meTagenomes☆65Updated 5 years ago
- A method of assessing sequence complexity based on kmer frequencies☆33Updated 7 years ago
- Benchmark datasets for WGS analysis☆39Updated 6 years ago
- Get microbial sequence data easier and faster☆28Updated 6 years ago
- REINDEER REad Index for abuNDancE quERy☆56Updated 4 months ago
- Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI☆29Updated 6 years ago
- De novo Extraction of Strains from MetAgeNomes☆71Updated 5 years ago
- Simka and SimkaMin are comparative metagenomics methods dedicated to NGS datasets.☆51Updated 3 years ago
- Efficient and comprehensive metadata acquisition from the NCBI databases (includes SRA).☆50Updated 3 years ago
- De novo estimates of genetic relatedness from next-gen sequencing data☆45Updated 6 years ago
- This is the codebase for Recycler, described in our manuscript: https://academic.oup.com/bioinformatics/article/33/4/475/2623362, by Roye…☆58Updated 4 years ago
- Workflows I find helpful for fungal genome annotation☆21Updated 2 years ago
- Fast and pretty dotplots for whole genomes assemblies using minimap and R/ggplot2☆76Updated 9 years ago
- VIRULIGN: fast codon-correct alignment and annotation of viral genomes☆35Updated 4 years ago
- Bioinformatics pipeline for nanopore sequencing data☆11Updated 6 years ago
- Metagenomic profiling and phylogenetic distances via common kmers☆42Updated 4 years ago