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Search results for shell fastq
fastq
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shell
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28 search results found
Juicer
⭐
313
A One-Click System for Analyzing Loop-Resolution Hi-C Experiments
Decona
⭐
23
fastq to polished sequenses: pipeline suitable for mixed samples and long (Nanopore) reads
Pfastq Dump
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22
parallel-fastq-dump implementation in bash script
Ikra
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21
RNAseq pipeline centered on Salmon
Assembler Components
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20
Components of genome sequence assembly tools
Tracespipe
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16
Reconstruction and analysis of viral and host genomes at multi-organ level
Sixess
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14
🔬🐛 Rapid 16s rRNA identification from isolate FASTQ files
Monorail External
⭐
13
examples to run monorail externally
Pipelines Wrappers
⭐
11
Shell wrappers for common NGS pipelines, RNAseq, ChIPseq, ATACseq, CUT&RUN/TAG, WGS, etc.
Fqless
⭐
11
less like viewer for fastq files
Cpg_me
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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)
Pgkb Ngs Pipeline
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10
PharmGKB NGS Pipeline
Guppy_on_slurm
⭐
10
Splitting and accelerating the Oxford Nanopore basecaller guppy using CPU with the SLURM job scheduler
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).
Circle_finder
⭐
8
Micro DNA identification
Atac Seq
⭐
8
ATAC-seq Pipeline in conjunction with Duygu Ucar & Jacques Banchereau Laboratories
Athlon
⭐
7
Accurate Typing of Human Leukocyte Antigen (HLA) by Oxford Nanopore Sequencing
Sentieon Dnascope Ml
⭐
7
Sentieon DNAscope + Machine Learning Model
Tagseq Qiime2 Snakemake
⭐
6
Pipeline to run qiime2 with snakemake
Ngs
⭐
6
Next-generation sequencing analysis pipelines & scrips
Tecandidates
⭐
6
TEcandidates
Fastq Info
⭐
6
Calculate fastq reads and sequencing coverage
Mergelanes
⭐
6
Merge fastq files split over lanes
Poolparty
⭐
5
Whole-genome bioinformatic pipeline for pooled or individual-based NGS data using bash and R
Leon
⭐
5
Leon - FASTA and FASTQ read compressor
Sentieon Google Genomics
⭐
5
Run Sentieon pipelines on Google Cloud Platform
Insilico_pcr
⭐
5
extract long read subsequences from a pair of primers
Downsampling
⭐
5
Downsample fastq files in an automated way
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