digo4 / Clinical-Genomics Star 13 Code Issues Pull requests Here we are going to discuss variant calling on human datasets using GATK Best practices pipeline picard samtools bwa-mem varscan bcftools bowtie2 trimgalore cutadapt fastqc freebayes fastp gatk4 trimmomatic gatk-bestpractices gatk-joint-variant-calling-workflow gatk-cnv gatk4-haplotypecaller Updated Jan 17, 2024 Shell
y9c / cutseq Sponsor Star 3 Code Issues Pull requests ✂️ Trim sequencing adapters from NGS data automatically adapter bioinformatics rna-seq ngs barcode umi dna-seq cutadapt Updated May 26, 2024 Python
Pinky-cloud224 / snakemake_workflow_rna_seq_data_analysis Star 1 Code Issues Pull requests config rna-seq jupyter-notebook conda python3 multiqc tpm salmon kallisto featurecounts paired-end fastq-files cutadapt fastqc htseq-count snakemake-workflow Updated Oct 20, 2022 Jupyter Notebook
hisplan / docker-cutadapt Star 0 Code Issues Pull requests Dockerized cutadapt docker cutadapt Updated Aug 4, 2021 Shell
DavideScarpetta / taxonomic_profiling Star 0 Code Issues Pull requests Metabarcoding analysis pipeline, using DADA2 and qiime2 bioinformatics bioinformatics-pipeline metabarcoding dada2 cutadapt qiime2 taxonomic-profiling metabarcoding-data Updated Jan 9, 2024 Shell
GenomicaMicrob / pair-end_cleaner Star 0 Code Issues Pull requests Script to unzip, clean, assemble, and convert illumina pair-end fastq files in all subdirectories for 16S amplicon data (V3, V4 and V3-V4 regions). metagenomics illumina 16s fastq-files cutadapt pair-end Updated Dec 13, 2018
cyverseuk / cutadapt Star 0 Code Issues Pull requests dockerfile bioinformatics hpc cyverseuk agaveapi hpc-applications cutadapt Updated May 8, 2017 Shell