20 results found Sort:

Nextomics
NextDenovo Nextomics
53
370
gpl-3.0
14
Fast and accurate de novo assembler for long reads
pacbio assembler long-reads genome-assembly oxford-nanopore
Created 2019-01-09
111 commits to master branch, last one 6 months ago
HKU-BAL
Clair3 HKU-BAL
29
249
unknown
11
Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling
pacbio genomics illumina nanopore ont-data long-reads ont-models deep-learning variant-calling variant-detection computational-biology
Created 2021-03-30
600 commits to main branch, last one 12 days ago
kishwarshafin
pepper kishwarshafin
42
244
mit
10
PEPPER-Margin-DeepVariant
nanopore variants long-reads pacbio-ccs oxford-nanopore variant-calling genome-variation assembly-polishing
Created 2019-05-10
1,281 commits to r0.8 branch, last one 2 years ago
GoekeLab
bambu GoekeLab
24
190
gpl-3.0
7
Reference-guided transcript discovery and quantification for long read RNA-Seq data
r bambu rna-seq nanopore long-reads bioconductor transcriptomics rna-seq-analysis nanopore-sequencing transcript-quantification transcript-reconstruction
Created 2020-02-07
2,159 commits to devel branch, last one about a month ago
broadinstitute
long-read-pipelines broadinstitute
24
142
bsd-3-clause
16
Long read production pipelines
wdl pipelines long-reads variant-calling de-novo-assembly
Created 2019-05-14
541 commits to main branch, last one 13 days ago
nf-core
taxprofiler nf-core
36
129
mit
156
Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
nf-core shotgun illumina nanopore nextflow pathogen pipeline workflow profiling long-reads microbiome metagenomics bioinformatics classification taxonomic-profiling taxonomic-classification
Created 2022-02-18
2,031 commits to master branch, last one 5 days ago
yangao07
abPOA yangao07
18
118
mit
8
abPOA: an SIMD-based C library for fast partial order alignment using adaptive band
simd banded-dp gfa-format long-reads alignment-graph consensus-sequence consensus-sequences partial-order-alignment multiple-sequence-alignment
Created 2018-02-11
262 commits to main branch, last one 7 days ago
GoekeLab
sg-nex-data GoekeLab
25
111
unknown
7
Nanopore RNA-Seq data from the Singapore Nanopore-Expression Project
rna-seq nanopore long-reads transcriptomics direct-rna-sequencing
Created 2019-02-28
300 commits to master branch, last one 4 days ago
MeHelmy
princess MeHelmy
8
79
mit
4
This repository has no description...
phasing long-reads methylation structural-variation single-nucleotide-variation
Created 2019-04-07
215 commits to master branch, last one 7 months ago
HKU-BAL
ClairS HKU-BAL
7
76
bsd-3-clause
6
ClairS - a deep-learning method for long-read somatic small variant calling
ont snvs indels pacbio phasing genomics illumina nanopore haplotypes long-reads short-reads deep-learning bioinformatics somatic-variants somatic-mutations long-read-sequencing
Created 2021-07-29
762 commits to main branch, last one 4 days ago
ganlab
GALA ganlab
17
74
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
bcgsc
straglr bcgsc
8
73
other
7
Tandem repeat expansion detection or genotyping from long-read alignments
genomics long-reads bioinformatics tandem-repeats
Created 2019-09-05
283 commits to master branch, last one 8 days ago
bcgsc
LINKS bcgsc
15
73
gpl-3.0
11
⛓ Long Interval Nucleotide K-mer Scaffolder
scaffold long-reads bloom-filter draft-assembly scaffold-layout genome-assemblies extract-kmer-pairs
Created 2015-05-11
610 commits to master branch, last one 11 months ago
natir
yacrd natir
8
72
mit
3
Yet Another Chimeric Read Detector
chimera sequence long-reads bioinformatics
Created 2018-03-28
183 commits to master branch, last one 26 days ago
katerinakazantseva
strainy katerinakazantseva
5
67
other
5
Graph-based assembly phasing
hifi assembly nanopore long-reads sequencing metagenomics long-read-sequencing metagenomic-analysis
Created 2021-12-29
517 commits to main branch, last one about a month ago
muellan
metacache muellan
11
57
gpl-3.0
7
memory efficient, fast & precise taxnomomic classification system for metagenomic read mapping
fasta fastq genome refseq taxonomy long-reads metagenomes ncbi-refseq metagenomics read-mapping dna-sequences bioinformatics classification metagenomic-data short-read-mapper bioinformatics-tool metagenomic-analysis genomic-data-analysis bioinformatics-algorithms metagenomic-classification
Created 2017-02-07
1,029 commits to master branch, last one 2 months ago
morispi
CONSENT morispi
5
55
agpl-3.0
4
Scalable long read self-correction and assembly polishing with multiple sequence alignment
msa ngs long self reads contigs assembly consensus polishing correction long-reads self-correction multiple-sequence-alignment
Created 2018-08-09
307 commits to master branch, last one 10 months ago
HKU-BAL
ClairS-TO HKU-BAL
3
51
bsd-3-clause
3
ClairS-TO - a deep-learning method for tumor-only somatic variant calling
ont snvs pacbio tumors genomics illumina nanopore variants long-reads tumor-only deep-learning bioinformatics variant-calling somatic-variants somatic-mutations long-read-sequencing
Created 2023-11-07
163 commits to main branch, last one a day ago
refresh-bio
colord refresh-bio
14
49
gpl-3.0
4
A versatile compressor of third generation sequencing reads.
pac-bio genomics long-reads sequencing compression fastq-files bioinformatics oxford-nanopore
Created 2021-06-17
22 commits to master branch, last one 12 months ago
CMU-SAFARI
SneakySnake CMU-SAFARI
11
49
gpl-3.0
9
SneakySnake:snake: is the first and the only pre-alignment filtering algorithm that works efficiently and fast on modern CPU, FPGA, and GPU architectures. It greatly (by more than two orders of magnit...
gpu fpga edlib minimap2 long-reads short-reads smith-waterman needleman-wunsch sequence-aligner sequence-alignment wavefront-alignment hardware-accelerator pre-alignment-filtering
Created 2019-09-22
73 commits to master branch, last one about a year ago