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The Top 23 Pipeline Fastq Open Source Projects

Open source projects categorized as Pipeline Fastq
Categories > Fastq
Categories > Data Processing > Pipeline
Juicer ⭐ 313
A One-Click System for Analyzing Loop-Resolution Hi-C Experiments
most recent commit a year ago
Bactopia ⭐ 281
A flexible pipeline for complete analysis of bacterial genomes
most recent commit 7 months ago
Zumis ⭐ 232
zUMIs: A fast and flexible pipeline to process RNA sequencing data with UMIs
most recent commit a year ago
Seq2science ⭐ 132
Automated and customizable preprocessing of Next-Generation Sequencing data, including full (sc)ATAC-seq, ChIP-seq, and (sc)RNA-seq workflows. Works equally easy with public as local data.
most recent commit 5 months ago
Viral Ngs ⭐ 129
Viral genomics analysis pipelines
most recent commit 4 years ago
Fetchngs ⭐ 93
Pipeline to fetch metadata and raw FastQ files from public and private databases
most recent commit 5 months ago
Pipeline Structural Variation ⭐ 87
Pipeline for calling structural variations in whole genomes sequencing Oxford Nanopore data
most recent commit 3 years ago
Scatac Pro ⭐ 64
A comprehensive tool for processing, analyzing and visulizing single cell chromatin accessibility sequencing data
most recent commit 10 months ago
Pyflow Chipseq ⭐ 55
a snakemake pipeline to process ChIP-seq files from GEO or in-house
most recent commit 4 years ago
Bamtofastq ⭐ 45
Convert 10x BAM files to the original FASTQs compatible with 10x pipelines
most recent commit 8 months ago
Ngs_pipeline ⭐ 31
Exome/Capture/RNASeq Pipeline Implementation using snakemake
most recent commit 6 years ago
Mpraflow ⭐ 27
A portable, flexible, parallelized tool for complete processing of massively parallel reporter assay data
most recent commit 3 months ago
Ublastx_stageone ⭐ 24
This is the source code for multisamples ARGs profiling using SARG2.0 database
most recent commit 3 years ago
Germline Dna ⭐ 23
A BioWDL variantcalling pipeline for germline DNA data. Starting with FASTQ files to produce VCF files. Category:Multi-Sample
most recent commit a year ago
Mapache ⭐ 23
mapping pipeline for ancient DNA
most recent commit 4 months ago
Allbiotc2 ⭐ 22
Benchmark pipeline for Structural Variation analyses, funded by the ALLBio.
most recent commit 10 years ago
Chip Seq_preprocess ⭐ 21
A preprocessing pipeline for ChIP-seq, including alignment, quality control, and visualization.
most recent commit 7 years ago
Natrix ⭐ 21
Open-source bioinformatics pipeline for the preprocessing of raw sequencing data.
most recent commit 2 years ago
Pipeline Umi Amplicon ⭐ 21
Workflow to prepare high accuracy single molecule consensus sequences from amplicon data using unique molecular identifiers
most recent commit a year ago
Rnaseq Nf ⭐ 20
RNAseq analysis pipeline
most recent commit 2 years ago
Pipelines ⭐ 20
RPD Pipelines
most recent commit 5 years ago
Rna Seq Snakemake ⭐ 20
Snakemake based pipeline for RNA-Seq analysis
most recent commit 5 years ago
Pipeline Nanopore Denovo Isoforms ⭐ 19
Pipeline for de novo clustering of long transcriptomic reads
most recent commit 2 years ago
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