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Tools List
Name of Tool | Name in CLI | Scientific Algorithms | Common Uses |
snpeff_annotate | SnpEff | Annotation | |
snpsift_annotate | SnpSift | Annotation |
Name of Tool | Name in CLI | Scientific Algorithms | Common uses |
aws_platform_to_s3_file_transfer | AWS S3 | ||
aws_s3_to_platform_files | AWS S3 | ||
sra_fastq_importer | Retrieve reads in FASTQ format from SRA |
Name of Tool | Name in CLI | Scientific Algorithms | Common Uses |
oqfe | WGS, WES- alignment and duplicate marking | ||
gatk4_bqsr_parallel | Variant calling | ||
bwa_mem_fastq_read_mapper | BWA-MEM | Short read alignment | |
gatk4_haplotypecaller_parallel | Variant calling, post-alignment QC | ||
gatk4_genotypegvcfs_single_sample_parallel | Variant calling | ||
picard_mark_duplicates | Variant Calling- remove duplicates, post-alignment | ||
strelka2_germline | Small variant calling, Germline, WGS, WES | ||
strelka2_somatic | Small variant calling, Somatic analysis |
Name of Tool | Name in CLI | Scientific Algorithms | Common Uses |
regenie | REGENIE | GWAS | |
plink_gwas | PLINK2 | ||
raremetal2 | RAREMETALWORKER, RAREMETAL | ||
saige_gwas_gbat | |||
saige_gwas_svat | |||
saige_gwas_grm | |||
saige_gwas_sparse_grm | |||
plink_pipeline | Plink2 | | |
plato_pipeline | Plato, Plink2 | | |
locuszoom | LocusZoom | GWAS, visualization |
Name of Tool | Name in CLI | Scientific Algorithms | Common Uses |
url_fetcher | N/A | Fetches a file from a URL onto the DNAnexus platform |
Name of Tool | Name in CLI | Scientific Algorithms | Common Uses |
sra_fastq_importer | Retrieve reads in FASTQ format from SRA | ||
url_fetcher | N/A | Fetches a file from a URL onto the DNAnexus platform |
Name of Tool | Name in CLI | Scientific Algorithms | Common Uses |
cloud_workstation | N/A | SSH-accessible unix shell on a platform cloud worker. Use it for ad hoc analysis of platform data. | |
ttyd | N/A | Unix shell on a platform cloud worker in your browser. Use it for ad hoc CLI operations and to launch https apps on 2 extra ports |
Name of Tool | Name in CLI | Scientific Algorithms | Common Uses |
glnexus | GLnexus | This app can also be used to create pVCF without running joint genotyping |
Name of Tool | Name in CLI | Scientific Algorithms | Common Uses |
picard_samtools_fasta_indexer | CreateSequenceDictionary command from the Picard suite of tools, samtools faidx from Samtools. | Read Mapping | |
picard_collect_multiple_metrics | QC- statistic metrics for mapped reads | ||
samtools_index | Building bam index file | ||
samtools_sort | Sort alignment result based on coordinates |
Name of Tool | Name in CLI | Scientific Algorithms | Common Uses |
phesant | PHESANT | PheWAS |
Name of Tool | Name in CLI | Scientific Algorithms | Common Uses |
prsice2 | PRSice-2 | Polygenic risk scores |
Name of Tool | Name in CLI | Scientific Algorithms | Common Uses |
multiqc | MultiQC | QC reporting | |
qualimap2_anlys | Qualimap2 | QC | |
rnaseqc | Transcriptomics Expression Quantification | ||
rseqc_rna_bam_eval | RSeQC | Transcriptomics Expression Quantification | |
fastqc | FastQC | ||
jellyfish_and_genomescope | Jellyfish, GenomeScope | k-mer counting |
Name of Tool | Name in CLI | Scientific Algorithms | Common Uses |
rsem | RSEM | Transcriptomics Expression Quantification | |
kallisto | Kallisto | Transcriptomics Expression Quantification | |
salmon_quant | Salmon | Transcriptomics Expression Quantification | |
salmon_mapping_quant | Salmon | Transcriptomics Expression Quantification |
Name of Tool | Name in CLI | Scientific Algorithms | Common Uses |
bowtie2_fasta_indexer | Bowtie 2: bowtie2-build | Building reference for Bowite2 alignment | |
bowtie2_fastq_read_mapper | bowtie2, samtools view, samtools sort, samtools index | Short read alignment | |
bwa_fasta_indexer | BWA- bwa index | Building reference for BWA alignment | |
minimap2_align_longread | minimap2, biobambam2 | Read Mapping of PacBio and ONT long reads | |
bwa_mem_fastq_read_mapper | BWA-MEM | Short read alignment | |
hisat2_index | Transcriptomics | ||
hisat2_mapper | Transcriptomics | ||
star_generate_genome_index | RNA Seq- indexing | ||
star_mapping | RNA Seq- mapping | ||
subread_feature_counts | featureCounts | Read summarization, RNAseq | |
star_generate_genome_index | Transcriptomics Expression Quantification | ||
star_mapping | Transcriptomics Expression Quantification | ||
salmon_index_builder | Salmon | Transcriptomics Expression Quantification | |
salmon_mapping_quant | Salmon | Transcriptomics Expression Quantification |
Name of Tool | Name in CLI | Scientific Algorithms | Common Uses |
gatk4_bqsr_parallel | Variant calling | ||
flexbar_fastq_read_trimmer | QC | ||
trimmomatic | Read quality trimming, adapter trimming |
Name of Tool | Name in CLI | Scientific Algorithms | Common Uses |
star_fusion_caller | RNA-Seq fusion calling | ||
gatk4_haplotypecaller_rnaseq | GATK best practice workflow for RNAseq short variant discovery (SNPs + Indels)(SplitNCigarReads, HaplotypeCaller, VariantFiltration) | RNA-seq variant calling, post-alignment QC | |
rnaseqc | Transcriptomics Expression Quantification | ||
rseqc_rna_bam_eval | RSeQC | Transcriptomics Expression Quantification | |
hisat2_index | Transcriptomics | ||
hisat2_mapper | Transcriptomics | ||
star_generate_genome_index | RNA Seq- indexing | ||
star_mapping | RNA Seq- mapping | ||
subread_feature_counts | featureCounts | Read summarization, RNAseq | |
star_generate_genome_index | Transcriptomics Expression Quantification | ||
star_mapping | Transcriptomics Expression Quantification | ||
salmon_index_builder | Salmon | Transcriptomics Expression Quantification | |
salmon_mapping_quant | Salmon | Transcriptomics Expression Quantification | |
kallisto_index_builder | Kallisto | Transcriptomics Expression Quantification | |
rsem | RSEM | Transcriptomics Expression Quantification | |
kallisto | Kallisto | Transcriptomics Expression Quantification | |
salmon_quant | Salmon | Transcriptomics Expression Quantification |
Name of Tool | Name in CLI | Scientific Algorithms | Common Uses |
Transcript_Expression_Part-02_Analysis-diff-exp_R.ipynb | DESeq2 | | |
Transcript_Expression_Part-03_Analysis-GSEA_R.ipynb | WebGestaltR | | |
Transcript_Expression_Part-04_Analysis-CoEx-Network_R.ipynb | WGCNA, topGO | | |
Transcript_Expression_Part-05_Analysis-Regulatory-Network_R.ipynb | GENIE3 | |
Name of Tool | Name in CLI | Scientific Algorithms | Common Uses |
transcriptomic_expression_quantification | FastQC, Trimmomatic, STAR, RSEM, Kallisto, Salmon, RNA-SeQC2, RSeQC, MultiQC |
Name of Tool | Name in CLI | Scientific Algorithm | Common Uses |
file_concatenator | N/A | ||
gzip | gzip | ||
swiss-army-knife | bcftools, bedtools, bgzip, plink, sambamba, samtools, seqtk, tabix, vcflib, Plato, QCTool, vcftools, plink2, Picard, REGENIE, BOLT-LMM, BGEN | Data processing tools | |
ttyd | N/A | Unix shell on a platform cloud worker in your browser. Use it for ad hoc CLI operations and to launch https apps on 2 extra ports |
Name of Tool | Name in CLI | Scientific Algorithms | Common Uses |
star_fusion_caller | RNA-Seq fusion calling | ||
gatk4_haplotypecaller_rnaseq | GATK best practice workflow for RNAseq short variant discovery (SNPs + Indels)(SplitNCigarReads, HaplotypeCaller, VariantFiltration) | RNA-seq variant calling, post-alignment QC | |
cnvkit_batch | Copy Number Variant | ||
deepvariant_germline | Variant calling | ||
parliament2 | Breakdancer, BreakSeq2, CNVnator, Delly, Lumpy, Manta, SVTyper, svviz, SURVIVOR | Structural variants | |
gatk4_haplotypecaller_parallel | Variant calling, post-alignment QC | ||
gatk4_genotypegvcfs_single_sample_parallel | Variant calling | ||
picard_mark_duplicates | Variant Calling- remove duplicates, post-alignment | ||
strelka2_germline | Small variant calling, Germline, WGS, WES | ||
strelka2_somatic | Small variant calling, Somatic analysis | ||
freebayes | Use for short variant calls | ||
gatk4_mutect2_variant_caller_and_filter | Somatic variant calling and post calling filtering | ||
gatk4_somatic_panel_of_normals_builder | Create a panel of normals (PoN) containing germline and artifactual sites for use with Mutect2. |
Name of Tool | Name in CLI | Scientific Algorithms | Common Uses |
locuszoom | LocusZoom | GWAS, visualization |
A Titan license is required to access and use these tools. Please contact DNAnexus Sales for more information.
Name of Tool | Name in CLI | Scientific Algorithms | Common Uses |
dxjupyterlab | dxpy, matplotlib, numpy, pandas, papermill, scipy, seaborn , dxdata, cntk, keras,scikit-learn, tensorflow, torch | Running analyses, visualizing data, building and testing models and algorithms in an interactive way | |
dxjupyterlab | dxpy, matplotlib, numpy, pandas, papermill, scipy, seaborn, dxdata, BiocManager, coloc, epiR, hyprcoloc, incidence, MendelianRandomization, outbreaks, prevalence | Running analyses, visualizing data, building and testing models and algorithms in an interactive way | |
dxjupyterlab | dxpy, matplotlib, numpy, pandas, papermill, scipy, seaborn, dxdata, BiocManager, coloc, epiR, hyprcoloc, incidence, MendelianRandomization, outbreaks, prevalence, Stata, stata_kernel | Running analyses, visualizing data, building and testing models and algorithms in an interactive way, accessing and manipulating data in spark databases and tables | |
dxjupyterlab | dxpy, matplotlib, numpy, pandas, papermill, scipy, seaborn , dxdata, nipype, freesurfer, FSL | Running imaging processing related analysis |
An Apollo license is required to access and use these tools. Please contact DNAnexus Sales for more information.
Name of Tool | Name in CLI | Scientific Algorithms | Common Uses |
data_model_loader_v2 | Dataset Creation | Dataset Creation | |
dataset-extender | Dataset Extension | Dataset Extension |
Name of Tool | Name in CLI | Scientific Algorithms | Common Uses |
csv-loader | N/A | Data Loading | |
spark-sql-runner | Spark SQL | Dynamic SQL Execution | |
table-exporter | N/A | Data Extraction |
Name of Tool |