fmalmeida / ngs-preprocess Star 30 Code Issues Pull requests Discussions A pipeline for preprocessing NGS data from Illumina, Nanopore and PacBio technologies workflow bioinformatics pipeline nextflow reproducible-research ngs reproducible-science pacbio illumina nanopack trimgalore ngs-preprocess bax2bam porechop pacbio-ccs Updated Jun 30, 2024 Nextflow
digo4 / Clinical-Genomics Star 27 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
hisplan / trimgalore Star 0 Code Issues Pull requests trimgalore modified version for prism trimgalore Updated Mar 15, 2017 Perl
PulmonomicsLab / mcdr-mtb-standalone-v2 Star 0 Code Issues Pull requests Multi-class classification of drug resistance in MTB clinical isolates machine-learning r vcf shell-script caret variant-calling samtools bwa-mem whole-genome-sequencing multiclass-classification trimgalore multilayer-perceptron freebayes explainable-ai shap mycobacterium-tuberculosis dalex drug-resistance-prediction Updated May 21, 2024 Shell
PulmonomicsLab / mcdr-mtb-standalone Star 0 Code Issues Pull requests Multi-class classification of drug resistance in MTB clinical isolates machine-learning svm prediction vcf diagnostics shell-script caret variant-calling samtools bwa-mem r-programming whole-genome-sequencing trimgalore multi-class-classification freebayes mycobacterium-tuberculosis drug-resistance-prediction Updated Jan 30, 2024 Shell