15 results found Sort:

MAGICS-LAB
DNABERT_2 MAGICS-LAB
67
293
apache-2.0
10
[ICLR 2024] DNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genome
dna covid genome splice dataset promoter promoters splice-site dna-training dna-processing language-model genome-analysis promoter-analysis transcription-factors transcription-factor-binding transcription-factor-binding-site
Created 2023-06-23
35 commits to main branch, last one 7 days ago
marbl
Winnowmap marbl
23
266
other
15
Long read / genome alignment software
pacbio nanopore genome-analysis
Created 2020-02-11
989 commits to master branch, last one about a month ago
biocommons
hgvs biocommons
94
248
apache-2.0
20
Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`
genomics variation sequencing bioinformatics genome-analysis variant-analysis
Created 2017-03-09
1,664 commits to main branch, last one 26 days ago
mbhall88
rasusa mbhall88
17
216
mit
6
Randomly subsample sequencing reads or alignments
bam rust fasta fastq random coverage alignment downsample subsampling bioinformatics genome-analysis
Created 2019-09-26
241 commits to main branch, last one 22 days ago
TobyBaril
EarlGrey TobyBaril
20
150
other
6
Earl Grey: A fully automated TE curation and annotation pipeline
genomics bioinformatics te-annotations genome-analysis genome-annotation transposable-elements
Created 2021-09-30
613 commits to main branch, last one 9 days ago
asntech
intervene asntech
28
136
other
6
Intervene: a tool for intersection and visualization of multiple genomic region and gene sets
pyton bedtools heatmaps intersection venn-diagram dna-sequences visualization genome-analysis
Created 2017-01-14
209 commits to master branch, last one about a year ago
fmalmeida
bacannot fmalmeida
9
100
gpl-3.0
4
Generic but comprehensive pipeline for prokaryotic genome annotation and interrogation with interactive reports and shiny app.
rgi barrnap phigaro nextflow pipeline prophages annotation ko-annotation genome-browser genome-analysis rrna-prediction virulence-genes virulence-factor insertion-sequences reproducible-research methylation-annotation mobile-genetic-elements genomic-islands-prediction prophage-sequences-prediction antimicrobial-genes-annotation
Created 2019-10-23
778 commits to master branch, last one about a month ago
ganlab
GALA ganlab
17
76
mit
4
Long-reads Gap-free Chromosome-scale Assembler
pacbio nanopore long-reads gap-filling scaffolding genome-analysis genome-assembly
Created 2020-04-01
30 commits to master branch, last one 2 years ago
moshi4
COGclassifier moshi4
6
58
mit
2
A tool for classifying prokaryote protein sequences into COG(Cluster of Orthologous Genes) functional category
cog python protein genomics visualization bioinformatics genome-analysis microbial-genomics functional-analysis comparative-genomics functional-annotation
Created 2022-03-18
92 commits to main branch, last one about a year ago
lynnlangit
TeamTeri lynnlangit
17
53
unknown
11
Bioinformatics on GCP, AWS or Azure
aws gcp gatk azure variants variant-calls bioinformatics cancer-genomics genome-analysis genome-sequencing genomics-analysis
Created 2016-10-04
561 commits to master branch, last one 6 months ago
CMU-SAFARI
RawHash CMU-SAFARI
5
50
gpl-3.0
8
RawHash can accurately and efficiently map raw nanopore signals to reference genomes of varying sizes (e.g., from viral to a human genomes) in real-time without basecalling. Described by Firtina et al...
rawhash seeding nanopore raw-signal hash-tables read-mapping segmentation contamination nanopore-data bioinformatics nanopore-reads event-detection genome-analysis nanopore-minion nanopore-sequencing relative-abundances nanopore-analysis-pipeline raw-nanopore-signal-analysis
Created 2023-01-20
46 commits to main branch, last one about a month ago
CMU-SAFARI
BLEND CMU-SAFARI
4
42
other
12
BLEND is a mechanism that can efficiently find fuzzy seed matches between sequences to significantly improve the performance and accuracy while reducing the memory space usage of two important applica...
blend minimizers strobemers fuzzy-seeds read-mapping spaced-seeds seed-matching bioinformatics genome-analysis genome-assembly de-novo-assembly read-overlapping
Created 2021-12-12
35 commits to master branch, last one about a year ago
NBChub
bgcflow NBChub
9
36
mit
2
Snakemake workflow for the analysis of biosynthetic gene clusters across large collections of genomes (pangenomes)
genome-analysis genome-annotation pangenome-pipeline biosynthetic-gene-clusters
Created 2021-09-13
812 commits to main branch, last one 15 days ago
brandonsaldan
codex brandonsaldan
1
28
other
3
A minimal genetic data explorer that processes all genetic information locally.
dna snpedia genetics bioinformatics genome-analysis
Created 2023-05-22
35 commits to main branch, last one about a year ago
linyuiz
zgtools linyuiz
3
25
unknown
2
zgtools: A pipeline that allows for the convenient acquisition of T2T (Telomere-to-Telomere) genomes.
t2t zgtools pipeline genome-analysis
Created 2024-05-20
325 commits to master branch, last one 10 days ago