fastqc

There are 0 repository under fastqc topic.

robertaboukhalil / fastq.bio
An interactive web tool for quality control of DNA sequencing data
bioinformatics fastqc genomics sequencing wasm webassembly
Language:Svelte 98
fastqc-rs / fastqc-rs
A quality control tool for FASTQ files written in rust
fastq sequence-quality fastqc k-mer-counting sequence-statistics
Language:Rust 32
angelovangel / faster
A (very) fast program for getting statistics about a fastq file, the way I need them, written in Rust
fastq-files ngs fastqc rust bioinformatics
Language:Rust 28
PavlidisLab / rnaseq-pipeline
RNA-seq pipeline for raw sequence alignment and transcript/gene quantification.
rna-seq alignment quantification ngs ngs-analysis illumina rsem star stringtie fastqc bioinformatics-pipeline bioinformatics gene-expression transcriptomics genomics spliced-alignment splice-aware bash
Language:Python 19
nf-core / hgtseq
A pipeline to investigate horizontal gene transfer from NGS data
nextflow nf-core pipeline workflow horizontal-gene-transfer ngs taxonomies bwa-mem bwa-mem2 fastqc genomics-visualization ggbio kraken2 krona multiqc samtools tidyverse
Language:Nextflow 18
ChillarAnand / fadapa
FAstqc DAta PArser - A minimal parser to parse FastQC output data.
python fastqc bioinformatics
Language:Jupyter Notebook 16
digo4 / Clinical-Genomics
Here we are going to discuss variant calling on human datasets using GATK Best practices pipeline
bcftools bowtie2 bwa-mem cutadapt fastp fastqc freebayes gatk-bestpractices gatk-cnv gatk-joint-variant-calling-workflow gatk4 gatk4-haplotypecaller picard samtools trimgalore trimmomatic varscan
Language:Shell 13
angelovangel / nxf-fastqc
A simple fastp-MultiQC nextflow pipeline
fastqc multiqc fastq-files ngs-pipeline nextflow-pipelines
Language:Nextflow 11
hanielcedraz / BAQCOM
Quality Control, Mapping and Reads Count for RNA-Seq Analysis
trimmomatic star quality-control rna-seq-analysis rna-seq-pipeline mapping rnaseqpipeline rna-seq-mapping rna-seq-qc bioinformatics bioinformatics-pipeline rna-seq-aligner multiqc fastqc hisat2 htseq-count featurecounts
Language:R 8
mnievesc / Ancient_mtDNA_Pipeline
Analysis pipeline for processing paired-end Illumina reads obtained after ancient mtDNA target enrichment capture.
ancient-dna-sequences fastq-files samtools bam-files pipeline mtdna bcftools bwa fastqc
Language:Shell 8
bixBeta / CFG
RNA-seq workflow for UALBANY CFG - Demux, QC, Vis, Align, preProcess, DGE Calls
illumina demultiplexing bcl2fastq fastqc multiqc star alignment homer
Language:R 4
BryanAbuchery / 16S-rRNA-End-to-End-Analysis
Qiime2 and DADA2 are one of the latest bioinformatics tools used in 16S RNA analysis. The current Qiime2 and DADA2 pipelines support End to End 16S RNA analysis, among other analyses.
qiime2 dada2 rna-analysis mock-analysis fastqc
Language:Shell 4
gustaveroussy / rna-count-kallisto
Estimate fastq-formatted read abundace in RNA-Seq analysis with Kallisto
snakemake-workflow snakemake bioinformatics reproducible-workflows kallisto fastqc multiqc conda json-schema
Language:Python 3
lvn3668 / fastqcparser
Python code to compute adatper content in reads, kmer content, per-base-GC content (at a specific position in a read alignment, against reference genome), per base NC content (at a specific position in a read alignment against the reference genome), per base seq quality (across aligned reads), per base sequence content, per base quality scores, per tile sequence quality
alignments fastqc ngs-analysis python reads
Language:Python 3
mehdimerbah / WES
Whole Exome Sequencing end-to-end pipeline. Starting from whole exome fastq files: Data QC, Adapter Trimming, Reference Genome Alignment, SAM/BAM Validation, Data Recalibration and Variant Calling.
variants quality-scores tile-quality fastqc quality whole-exome-sequencing trimmomatic ngs-pipeline
Language:HTML 3
sequana / fastqc
sequana pipeline to perform parallel fastqc and summarize results with multiqc plot
fastqc ngs sequana snakemake
Language:Python 3
tdayris-perso / wes-mapping-bwa-gatk
Map and post-process your bams for SNP calling
snakemake-workflows bioinformatics-pipeline reproducible-research whole-exome-sequencing bwa gatk4 fastqc multiqc
Language:Python 2
wucc009 / Platelet_transcriptome_fastq_data_processing
血小板转录组fastq数据处理
geo ena sra linux aria2c bwa ensemble fastp fastqc htseq-count r rpm star tpm trimmomatic circbank ciri2 fastq
Language:Shell 2
yejg2017 / Sequence-Mapping-Bio
This is a code tutorial for rna or dna sequence mapping by myself-RyanYip
fastqc htseq salmon star bowtie2 featurecounts multiqc
Language:Shell 2
IMS-Bio2Core-Facility / polya_liftover
A Snakemake Workflow for using PolyA_DB and UCSC LiftOver with CellRanger
bioinformatics-pipeline snakemake cellranger liftover workflow single-cell-rna-seq reproducibility python shell transcriptomics fastqc multiqc
Language:Python 1
kashiff007 / RNA-seq-Pipeline-Under-Construction-
Complete Pipeline for RNA-seq data analysis: From FastQ to differntial gene expression to annotated Variations.
rna-seq pipeline next-generation-sequencing variant-calling mapping reads snp differential-gene-expression fastq fastqc bioinformatics illumina genomics transcriptomics bash
Language:Shell 1
kevin-wamae / snakemake-illumina-fastqc
A Snakemake workflow for quality control assessment of Illumina NGS data using FastQC and MultiQC
fastqc multiqc quality-control snakemake trimming
Language:Python 1
Moha-cm / RNAseq-Analysis
Bulk Rna-seq Analysis
bash-script bwa fastqc r r-markdown rna-seq-analysis trimmomatic featurescount deseq2-analysis gdc-portal gene-expression getx tcga
Language:HTML 1
nbay13 / toilkit
A python package for working with inputs to and outputs from the toil-rnaseq pipeline
rnaseq-pipeline transcriptomics bioinformatics rnaseq rsem fastqc sequence-alignment
Language:Python 1
NorwegianVeterinaryInstitute / DemultiplexRawSequenceData
A workflow automation script: demultiplex the library sequence, run quality checks, deliver to archiving and processing afterwards
bioinformatics bioinformatics-analysis bioinformatics-pipeline bioinformatics-scripts bioinformatics-tool fastqc multiqc python3
Language:Python 1
Pinky-cloud224 / snakemake_workflow_rna_seq_data_analysis
conda config cutadapt fastq-files fastqc featurecounts htseq-count jupyter-notebook kallisto multiqc paired-end python3 rna-seq salmon snakemake-workflow tpm
Language:Jupyter Notebook 1
tdayris-perso / rna-count-salmon
Snakemake workflow for Salmon quantification and FastQC quality controls
snakemake-workflows bioinformatics-pipeline reproducible-workflows rnaseq-pipeline fastqc salmon multiqc
Language:Python 1
adityamahadevaniyer / Cut-and-Tag
Slurm scripts for analyzing bulk Cutandtag data
cutandtag bowtie2 deeptools fastqc trimmomatic picard slurm
Language:Shell 0
alex-merge / PyFastaTools
Tools to analyze fasta or fastaq files with python.
fasta fasta-sequences fastq fastq-files fastqc quality-check sequence
Language:Python 0
anita-brzoza / university_projects
The repository contain directories of projects done during the bioinformatics degree program
fastqc bowtie2 data-analysis gatk multiqc samtools trimmomatic vcftools bioinformatics bioinformatics-pipeline smith-waterman-algorithm
Language:HTML 0
OrangePomeranian / Pipeline_with_Snakemake
Genomic Analysis Pipeline: Automate data preprocessing, variant calling, and annotation with Snakemake. Ensure reproducibility and reliability in genomic studies.
bioinformatics-pipeline bwa fastqc raport snakemake snpeff variant-calling
Language:HTML 0
alitermos / FastQC_processor
A script that efficiently processes multiple '.fastq' files, automatically organizing the pre-trimmed output into a folder named 'qc_reports_pretrim' for streamlined quality control and sequence data analysis.
bioinformatics-scripts fastqc
Language:Shell
Fatemehrshd / RNA-Seq-Analysis
bioinformatics fastqc hisat htseq htseq-count r read-mapping rna-sequencing samtools trimmomatic
Language:Jupyter Notebook
ineelhere / bioinformatics
Exploring Bioinformatics pipelines
nextflow bioinformatics rna-seq multiqc fastqc
Language:HTML
julianneyang / transcriptomicsonhoffman
Walks through installation and usage of FASTQC, MultiQC, Trimmomatic, and Salmon for transcriptomic data preprocessing. Includes Grid Engine shell scripts that can be looped over many files in a directory.
fastqc hpc multiqc rnaseq salmon transcriptomics trimmomatic
Language:R
mattgalbraith / fastqc-docker-singularity
Build Docker container for FastQC software and (optionally) convert to Apptainer/Singularity.
apptainer bioinformatics docker fastqc singularity
Language:Dockerfile

fastqc

robertaboukhalil / fastq.bio

fastqc-rs / fastqc-rs

angelovangel / faster

PavlidisLab / rnaseq-pipeline

nf-core / hgtseq

ChillarAnand / fadapa

digo4 / Clinical-Genomics

angelovangel / nxf-fastqc

hanielcedraz / BAQCOM

mnievesc / Ancient_mtDNA_Pipeline

bixBeta / CFG

BryanAbuchery / 16S-rRNA-End-to-End-Analysis

gustaveroussy / rna-count-kallisto

lvn3668 / fastqcparser

mehdimerbah / WES

sequana / fastqc

tdayris-perso / wes-mapping-bwa-gatk

wucc009 / Platelet_transcriptome_fastq_data_processing

yejg2017 / Sequence-Mapping-Bio

IMS-Bio2Core-Facility / polya_liftover

kashiff007 / RNA-seq-Pipeline-Under-Construction-

kevin-wamae / snakemake-illumina-fastqc

Moha-cm / RNAseq-Analysis

nbay13 / toilkit

NorwegianVeterinaryInstitute / DemultiplexRawSequenceData

Pinky-cloud224 / snakemake_workflow_rna_seq_data_analysis

tdayris-perso / rna-count-salmon

adityamahadevaniyer / Cut-and-Tag

alex-merge / PyFastaTools

anita-brzoza / university_projects

OrangePomeranian / Pipeline_with_Snakemake

alitermos / FastQC_processor

Fatemehrshd / RNA-Seq-Analysis

ineelhere / bioinformatics

julianneyang / transcriptomicsonhoffman

mattgalbraith / fastqc-docker-singularity