C++ htslib/bwa-mem/fermi interface for interrogating sequence data
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Aug 9, 2024 - C++
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bwa-mem
Here are 27 public repositories matching this topic...
BWA-MEME: Faster BWA-MEM2 using learned-index
machine-learning bioinformatics genomics ngs bwa-mem alignment-algorithm learned-index bwa-mem2 short-read-mapping bwa-meme
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Jul 1, 2024 - C++
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
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Jan 17, 2024 - Shell
Sentieon DNAseq
acceleration gatk bioinformatics-pipeline variant-calling dnaseq bwa-mem dna-sequencing sentieon gatk4 genomics-data
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Dec 30, 2020 - Shell
Optimised pipeline to process whole genome sequence data from fastq to BAM on NCI Gadi
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Aug 12, 2022 - Shell
Detecting transposable element invasions without repeat library. Detects also horizontal transfer events and endogenized viruses. All you need is a reference genome and some short reads
genome fasta fastq bedtools samtools genome-analysis bwa-mem transposons genome-assembly multiple-sequence-alignment transposable-element consensus-sequences
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Nov 25, 2024 - Shell
The DKFZ alignment workflow plugin originally developed at the eilslabs
workflow bam-files quality-control alignment wes wgbs bwa bwa-mem conda-environment fastq-files roddy
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Oct 5, 2023 - Python
vSNP -- validate SNPs
bam-files snps pipeline genomics phylogenetics influenza wgs high-throughput-sequencing bwa-mem tuberculosis whole-genome-sequencing analysis-pipeline vcf-files mycobacterium-bovis mycobacterium-tuberculosis-complex mycobacterium-bovis-af2122 brucella freebayes sars-cov-2
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Oct 1, 2024 - Python
Collecting Genotypes from ENA and make their SNPs
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Sep 27, 2021 - Python
Small GATK alignment and variant calling pipeline using python
pipeline genomics parallel vcf python-wrapper alignment population population-genomics variant-calling bwa bwa-mem gatk4
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Jul 18, 2022 - Python
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Jul 30, 2020 - Python
This repository will house the scripts used to analyze and represent genomic and temperature data for my dissertation.
ggplot2 bioinformatics snps scripts awk temperature bioinformatics-pipeline samtools bwa-mem bash-scripting snvs awk-script mutect2 mitochondria mitochondrial-variants mitochondrial-genomes
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Oct 2, 2022 - Shell
Fast bwa-mem dna matching algor implemented in system verilog, fully synthesizable.
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Apr 9, 2022 - Stata
The second part of https://github.com/npanuhin/BIOCAD
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Mar 12, 2021 - Python
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
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May 21, 2024 - Shell
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