bwa-mem

There are 0 repository under bwa-mem topic.

walaj / SeqLib
C++ htslib/bwa-mem/fermi interface for interrogating sequence data
bwa-mem fermi htslib c-plus-plus sequence-alignments
Language:C++ 133
kaist-ina / BWA-MEME
BWA-MEME: Faster BWA-MEM2 using learned-index
alignment-algorithm bioinformatics bwa-mem bwa-mem2 bwa-meme genomics learned-index machine-learning ngs short-read-mapping
Language:C++ 102
Sentieon / sentieon-dnaseq
Sentieon DNAseq
acceleration bioinformatics-pipeline bwa-mem dna-sequencing dnaseq gatk gatk4 genomics-data sentieon variant-calling
Language:Shell 20
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 19
Sydney-Informatics-Hub / Fastq-to-BAM
Optimised pipeline to process whole genome sequence data from fastq to BAM on NCI Gadi
bioinformatics sequencing ngs mapping bwa-mem gatk-bestpractices
Language:Shell 18
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
DKFZ-ODCF / AlignmentAndQCWorkflows
The DKFZ alignment workflow plugin originally developed at the eilslabs
workflow bwa wgbs quality-control alignment fastq-files roddy wes bwa-mem bam-files conda-environment
Language:Python 7
qingxiangguo / Tools-for-Cancer-Genome-Analysis
Installation and usage for various tools for cancer genomics
alignment arriba bioinformatics bwa-mem cancer conda fasterq-dump mamba picard sam samtools star tricks
Language:Python 7
cancerit / dockstore-cgpmap
Mapping using PCAP
bwa-mem biobambam2
Language:Common Workflow Language 6
rpianezza / GenomeDelta
Library-free horizontal transfer detection, with a focus on transposable element invasions
bedtools bwa-mem consensus-sequences fasta fastq genome genome-analysis genome-assembly multiple-sequence-alignment samtools transposable-element transposons
Language:Shell 6
AmirHoseinSafari / Genotype-collector-and-SNP-dataset-creator
Collecting Genotypes from ENA and make their SNPs
snp gatk samtools ena genotype tuberculosis bwa-mem fastq-files isolate snp-calling
Language:Python 5
bioinfo-pf-curie / mpiBWA
bwa-mem threads parallel mpirun mpi alignment
Language:C 5
broadinstitute / gatk-bwamem-jni
JNI code for bwa mem
bwa jni bwamem bwa-mem aligner
Language:Java 3
AntoineHo / runGATK
Small GATK alignment and variant calling pipeline using python
gatk4 parallel python-wrapper variant-calling alignment bwa bwa-mem pipeline vcf genomics population population-genomics
Language:Python 2
LidiaGS / g-d_algorithm
bioinformatics-pipeline bwa bwa-mem samtools
Language:Python 2
USDA-VS / vSNP3
vSNP -- validate SNPs
bam-files snps analysis-pipeline brucella freebayes genomics high-throughput-sequencing influenza mycobacterium-tuberculosis-complex phylogenetics pipeline sars-cov-2 tuberculosis vcf-files wgs whole-genome-sequencing mycobacterium-bovis mycobacterium-bovis-af2122 bwa-mem
Language:Python 2
phdscripts
asw0049 / phdscripts
This repository will house the scripts used to analyze and represent genomic and temperature data for my dissertation.
bash-scripting bioinformatics bioinformatics-pipeline ggplot2 scripts snps snvs temperature bwa-mem mitochondria mitochondrial-genomes mitochondrial-variants mutect2 samtools awk awk-script
Language:Shell 1
loykylewong / bwa-mem-fpga
Fast bwa-mem dna matching algor implemented in system verilog, fully synthesizable.
axi-stream bwa-mem dna
Language:Stata 1
FaithGriffin / CandidaPhylo
Focused on constructing a phylogenetic tree from Philippine strains of Candida albicans.
candida-albicans wdl-workflow cromwell docker docker-image dockstore json picard bwa-mem samtools
Language:WDL 0
idrissrasheed / Variant-Calling-Pipeline
Created a pipeline to carry out the alignment of a reference genome to the creation of a variant calling format (VCF).
bash bash-script bwa-mem variant-calling
Language:Shell 0
PulmonomicsLab / mcdr-mtb-standalone
Multi-class classification of drug resistance in MTB clinical isolates
bwa-mem caret diagnostics drug-resistance-prediction freebayes machine-learning multi-class-classification mycobacterium-tuberculosis prediction r-programming samtools shell-script svm trimgalore variant-calling vcf whole-genome-sequencing
Language:Shell 0
cnr-ibba / nf-resequencing-mem
Nextflow resequencing pipeline with bwa-mem and freebayes
nextflow-pipeline resequencing bwa-mem freebayes nextflow nextflow-dsl2 bcftools
Language:Nextflow
crisprVerse / Rbwa
R wrapper for BWA-backtrack and BWA-MEM aligners
alignment bwa bwa-mem dna-sequences dna-sequencing
Language:C
Grelot / reserveBenefit--snpsdata_analysis
Codes i wrote for the paper "genomic resources for Mediterranean fishes"
bash bcftools bedtools bwa-mem container genome htslib python3 r radseq reservebenefit samtools singularity snp vcftools
Language:Shell
npanuhin / BIOCAD-BWA
The second part of https://github.com/npanuhin/BIOCAD
bwa bwa-mem genomes genomes-comparison
Language:Python