Search Results - RepositoryStats

334

1.9k

mit

51

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

qc ngs umi fastq polyg filter adapter merging overlap quality illumina trimming filtering splitting sequencing duplication preprocessing bioinformatics quality-control

Created 2017-10-31

465 commits to master branch, last one 5 days ago

spades ablab

139

765

other

32

SPAdes Genome Assembler

illumina sequencing genome-assembly sequence-assembler metagenome-assembly transcriptome-assembly next-generation-sequencing

Created 2016-06-01

15,108 commits to main branch, last one 27 days ago

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

genomics igordot

54

200

unknown

7

A collection of scripts and notes related to genomics and bioinformatics

dna gtf vcf fast5 fasta fastq science genomics illumina nanopore workflow sequencing bioinformatics

Created 2015-12-22

118 commits to master branch, last one 26 days ago

viral-ngs broadinstitute

67

189

other

30

Viral genomics analysis pipelines

bam fastq viral genome genomics illumina viral-ngs genome-assembly variant-calling genome-sequencing variant-annotations

Created 2014-09-25

3,233 commits to master branch, last one 2 months ago

ampliseq nf-core

119

188

mit

153

Amplicon sequencing analysis workflow using DADA2 and QIIME2

16s 18s its edna rrna pacbio qiime2 nf-core illumina nextflow pipeline workflow iontorrent microbiome metagenomics metabarcoding amplicon-sequencing taxonomic-profiling taxonomic-classification

Created 2018-09-26

2,541 commits to master branch, last one 18 days ago

strobealign ksahlin

17

151

mit

10

Aligns short reads using dynamic seed size with strobemers

illumina alignment strobemers bioinformatics short-read-mapping

Created 2021-05-23

1,679 commits to main branch, last one 4 days ago

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

viralrecon nf-core

113

125

mit

108

Assembly and intrahost/low-frequency variant calling for viral samples

ont artic viral virus covid19 nf-core amplicon assembly covid-19 illumina nanopore nextflow pipeline workflow sars-cov-2 metagenomics oxford-nanopore variant-calling long-read-sequencing

Created 2020-03-30

2,788 commits to master branch, last one about a year ago

xTea parklab

23

102

other

9

Comprehensive TE insertion identification with WGS/WES data from multiple sequencing technics

pacbio illumina nanopore linked-reads transposable-elements mobile-element-insertion

Created 2018-07-12

144 commits to master branch, last one about a year ago

wengan adigenova

14

84

agpl-3.0

7

An accurate and ultra-fast hybrid genome assembler

hybrid pacbio illumina nanopore genome-assembler

Created 2019-03-04

50 commits to master branch, last one 3 years ago

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

fq stjude-rust-labs

5

76

mit

15

Command line utility for manipulating Illumina-generated FASTQ files.

rust fastq genomics illumina fastq-files bioinformatics next-generation-sequencing

Created 2018-03-12

449 commits to master branch, last one 12 days ago

sns igordot

26

64

mit

8

Analysis pipelines for genomic sequencing data

dna nyu wes wgs rrbs wgbs rna-seq analysis atac-seq genomics illumina pipeline sequencing bioinformatics

Created 2016-08-24

173 commits to main branch, last one 2 months ago

aldy 0xTCG

20

59

other

5

Allelic decomposition and exact genotyping of highly polymorphic and structurally variant genes

adme allele cyp2d6 pgrnseq genotype illumina sequencing bioinformatics

Created 2017-12-14

417 commits to master branch, last one 24 days ago

MpGAP fmalmeida

11

57

gpl-3.0

4

Multi-platform genome assembly pipeline for Illumina, Nanopore and PacBio reads

canu flye pilon pacbio polish spades illumina nanopore nextflow pipeline workflow unicycler genome-assembly hybrid-assemblies reproducible-science reproducible-research

Created 2019-08-06

477 commits to master branch, last one 2 months ago

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

demultiplex nf-core

38

45

mit

97

Demultiplexing pipeline for sequencing data

nf-core illumina nextflow pipeline workflow bcl2fastq bases2fastq demultiplexing elementbiosciences

Created 2020-03-05

1,145 commits to master branch, last one 27 days ago