Score Assemblies
Snakemake workflow for scoring and comparing multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s)
| Project Name | Stars | Downloads | Repos Using This | Packages Using This | Most Recent Commit | Total Releases | Latest Release | Open Issues | License | Language |
|---|---|---|---|---|---|---|---|---|---|---|
| Deepvariant | 2,978 | 5 months ago | 8 | bsd-3-clause | Python | |||||
| DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data. | ||||||||||
| Gatk | 1,576 | 2 | 2 months ago | 46 | March 16, 2023 | 1,299 | other | Java | ||
| Official code repository for GATK versions 4 and up | ||||||||||
| Hail | 905 |  | 17 | 3 months ago | 146 | October 30, 2023 | 211 | mit | Python | |
| Cloud-native genomic dataframes and batch computing | ||||||||||
| Ncbi Genome Download | 784 |  | 2 | 6 | 9 months ago | 25 | July 28, 2023 | 38 | apache-2.0 | Python |
| Scripts to download genomes from the NCBI FTP servers | ||||||||||
| Jcvi | 650 |  | 1 | 1 | 4 months ago | 97 | August 30, 2023 | 41 | bsd-2-clause | Python |
| Python library to facilitate genome assembly, annotation, and comparative genomics | ||||||||||
| Bowtie2 | 594 | 4 months ago | 143 | gpl-3.0 | C++ | |||||
| A fast and sensitive gapped read aligner | ||||||||||
| Nanopolish | 496 | 9 months ago | 60 | mit | C++ | |||||
| Signal-level algorithms for MinION data | ||||||||||
| Sniffles | 479 | 4 months ago | 8 | July 27, 2023 | 95 | mit | Python | |||
| Structural variation caller using third generation sequencing | ||||||||||
| Hifiasm | 443 | 3 months ago | 324 | mit | C++ | |||||
| Hifiasm: a haplotype-resolved assembler for accurate Hifi reads | ||||||||||
| Megahit | 442 | a year ago | 78 | gpl-3.0 | C++ | |||||
| Ultra-fast and memory-efficient (meta-)genome assembler | ||||||||||
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Python
Assembly
Bioinformatics
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