Data

Tools

Indexes

Applications

Experiments

Open Sustainable Technology

https://github.com/xiaoli-dong/pathogenseq

Pathogen whole genome sequence (WGS) data analysis pipeline
amr assembly capsular-typing emm-typing illumina mlst nanopore ngs pathogen plasmid serotyping taxonomy virulome
Added: over 1 year ago - Last Synced: 11 months ago - Created: June 28, 2023

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: Nextflow
  • Commits: 151
  • Committers: 5
  • Issues: 1
  • Pull Requests: 0
https://github.com/fulcrumgenomics/fgbio

Tools for working with genomic and high throughput sequencing data.
analyzing-genomic-data bioinformatics fgbio genomics molecular-indexes ngs scala umi
Added: over 1 year ago - Last Synced: 11 months ago - Created: March 03, 2016

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: Scala
  • Commits: 646
  • Committers: 17
  • Issues: 112
  • Pull Requests: 73
https://github.com/afrendeiro/toolkit

A toolkit for NGS analysis with Python
atac-seq bioinformatics chip-seq looper ngs ngs-analysis project-management pypiper rna-seq
Added: over 1 year ago - Last Synced: 11 months ago - Created: May 30, 2017

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: Python
  • Commits: 680
  • Committers: 3
  • Issues: 55
  • Pull Requests: 14
  • Owner: afrendeiro
  • Stars: 13
  • Forks: 4
  • Packages: 1
  • Downloads: 137
https://github.com/cokelaer/damona

singularity environment manager (application to NGS and bioinformatics)
bioinformatics conda manager ngs singularity
Added: over 1 year ago - Last Synced: 11 months ago - Created: July 24, 2020

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: Python
  • Commits: 501
  • Committers: 3
  • Issues: 41
  • Pull Requests: 19
  • Owner: cokelaer
  • Stars: 5
  • Forks: 2
  • Packages: 1
  • Downloads: 146
https://github.com/bioconvert/bioconvert

Bioconvert is a collaborative project to facilitate the interconversion of life science data from one format to another.
bam2cram bam2sam bcf2vcf bigbed2bed bioinformatics conversion convertor cram2bam cram2sam embl2ena embl2fasta embl2genbank fasta2fastq genbank2embl genbank2fasta ngs phylogeny sam2bam sequence sniffer
Added: over 1 year ago - Last Synced: 11 months ago - Created: October 11, 2017

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: Python
  • Commits: 1715
  • Committers: 33
  • Issues: 47
  • Pull Requests: 62
  • Owner: bioconvert
  • Stars: 351
  • Forks: 42
  • Packages: 1
  • Downloads: 286
https://github.com/daylily-informatics/daylily

A NGS analysis framework for WGS data, which automates the entire process of spinning up AWS EC2 spot instances and processing FASTQ to snvVCF in <60m, for dollars a sample and achieving Fscores of 0.998.
aws bioinformatics bioinformatics-pipeline budgeting ec2 ephemeral genomic-data-analysis giab human-genome informatics ngs parallel-cluster scalable scaling slurm snakemake snv-call wgs
Added: over 1 year ago - Last Synced: 11 months ago - Created: April 29, 2023

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: Python
  • Commits: 313
  • Committers: 12
  • Issues: 0
  • Pull Requests: 17
https://github.com/epigen/spilterlize_integrate

A Snakemake workflow to split, filter, normalize, integrate and select highly variable features of count matrices resulting from experiments with sequencing readout (e.g., RNA-seq, ATAC-seq, ChIP-seq, Methyl-seq, miRNA-seq,...) including diagnostic visualizations.
atac-seq batch-effect bioinformatics biomedical-data-science chip-seq count-matrix dimensionality-reduction integration ngs normalization pipeline rna-seq snakemake visualization workflow
Added: over 1 year ago - Last Synced: 11 months ago - Created: June 28, 2023

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: Python
  • Commits: 22
  • Committers: 2
  • Issues: 7
  • Pull Requests: 0
  • Owner: epigen
  • Stars: 8
  • Forks: 0
  • Packages: 0
https://github.com/bioforensics/microhapulator

Tools for empirical microhaplotype calling, forensic interpretation, and simulation.
bioinformatics forensics hacktoberfest microhaplotypes ngs
Added: over 1 year ago - Last Synced: 11 months ago - Created: October 10, 2018

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: Python
  • Commits: 227
  • Committers: 6
  • Issues: 44
  • Pull Requests: 75
  • Owner: bioforensics
  • Stars: 6
  • Forks: 1
  • Packages: 1
  • Downloads: 6
https://github.com/baku4/sigalign

A Similarity-Guided Alignment Algorithm
algorithm bioinformatics next-generation-sequencing ngs sequence-alignment
Added: over 1 year ago - Last Synced: 11 months ago - Created: June 18, 2021

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: Rust
  • Commits: 412
  • Committers: 4
  • Issues: 0
  • Pull Requests: 7
  • Owner: baku4
  • Stars: 10
  • Forks: 1
  • Packages: 2
  • Downloads: 2,682
https://github.com/pepkit/looper

A job submitter for Portable Encapsulated Projects
bioinformatics bioinformatics-pipeline ngs pipeline-submission-engine
Added: over 1 year ago - Last Synced: 11 months ago - Created: November 16, 2017

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: Python
  • Commits: 2606
  • Committers: 23
  • Issues: 195
  • Pull Requests: 104
  • Owner: pepkit
  • Stars: 19
  • Forks: 7
  • Packages: 2
  • Downloads: 410
https://github.com/bishop-laboratory/rlpipes

RLPipes: A standardized R-loop-mapping pipeline.
bioinformatics ngs pipeline r-loop snakemake
Added: over 1 year ago - Last Synced: 11 months ago - Created: June 03, 2020

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: Python
  • Commits: 246
  • Committers: 4
  • Issues: 70
  • Pull Requests: 21