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The Top 23 Shell Fastq Open Source Projects

Open source projects categorized as Shell Fastq
Juicer ⭐ 313
A One-Click System for Analyzing Loop-Resolution Hi-C Experiments
most recent commit a year ago
Decona ⭐ 23
fastq to polished sequenses: pipeline suitable for mixed samples and long (Nanopore) reads
most recent commit 2 years ago
Pfastq Dump ⭐ 22
parallel-fastq-dump implementation in bash script
most recent commit 4 years ago
Ikra ⭐ 21
RNAseq pipeline centered on Salmon
most recent commit a year ago
Assembler Components ⭐ 20
Components of genome sequence assembly tools
most recent commit 2 years ago
Tracespipe ⭐ 16
Reconstruction and analysis of viral and host genomes at multi-organ level
most recent commit 10 months ago
Sixess ⭐ 14
🔬🐛 Rapid 16s rRNA identification from isolate FASTQ files
most recent commit 6 years ago
Monorail External ⭐ 13
examples to run monorail externally
most recent commit 4 months ago
Pipelines Wrappers ⭐ 11
Shell wrappers for common NGS pipelines, RNAseq, ChIPseq, ATACseq, CUT&RUN/TAG, WGS, etc.
most recent commit 7 months ago
Fqless ⭐ 11
less like viewer for fastq files
most recent commit 5 years ago
Cpg_me ⭐ 10
A whole genome bisulfite sequencing (WGBS) pipeline for the alignment and QC of DNA methylation that goes from from raw reads (FastQ) to a CpG count matrix (Bismark cytosine reports)
most recent commit 2 years ago
Pgkb Ngs Pipeline ⭐ 10
PharmGKB NGS Pipeline
most recent commit 6 years ago
Guppy_on_slurm ⭐ 10
Splitting and accelerating the Oxford Nanopore basecaller guppy using CPU with the SLURM job scheduler
most recent commit 2 years ago
Ensemblevariantcallingpipeline ⭐ 10
The EnsembleVariantCallingPipeline takes files in FASTQ or BAM format and performs SNV and INDEL variant calling from 4 variant callers (Mutect2, Strelka2, Varscan2, MuSE) and indel variant calling from 3 variant callers (Mutect2, Strelka2, Varscan2).
most recent commit a year ago
Circle_finder ⭐ 8
Micro DNA identification
most recent commit 3 years ago
Atac Seq ⭐ 8
ATAC-seq Pipeline in conjunction with Duygu Ucar & Jacques Banchereau Laboratories
most recent commit 5 years ago
Athlon ⭐ 7
Accurate Typing of Human Leukocyte Antigen (HLA) by Oxford Nanopore Sequencing
most recent commit 6 years ago
Sentieon Dnascope Ml ⭐ 7
Sentieon DNAscope + Machine Learning Model
most recent commit 2 years ago
Tagseq Qiime2 Snakemake ⭐ 6
Pipeline to run qiime2 with snakemake
most recent commit 4 years ago
Ngs ⭐ 6
Next-generation sequencing analysis pipelines & scrips
most recent commit 3 years ago
Tecandidates ⭐ 6
TEcandidates
most recent commit 2 years ago
Fastq Info ⭐ 6
Calculate fastq reads and sequencing coverage
most recent commit 4 years ago
Mergelanes ⭐ 6
Merge fastq files split over lanes
most recent commit 6 years ago
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