Apps and workflows available on DNAnexus

App library

The following apps are available as apps in the App Library on the platform.

NameDescription
BamTools Mappings MergerMerges multiple BAM files into a single one (link)
Bowtie2 FASTA IndexerIndexes a FASTA reference genome sequence for downstream use by the Bowtie2 mapping app (link)
Bowtie2 FASTQ Read MapperMaps FASTQ reads (paired or unpaired) to a reference genome with the Bowtie 2 software (link)
BWA FASTA IndexerIndexes a FASTA reference genome sequence for downstream use by the BWA-backtrack and BWA-MEM mapping apps (link)
BWA-backtrack FASTQ Read MapperMaps FASTQ reads (paired or unpaired) to a reference genome with the BWA-backtrack algorithm (link)
BWA-MEM FASTQ Read MapperMaps FASTQ reads (paired or unpaired) to a reference genome with the BWA-MEM algorithm (link)
CNVkitCall copy number variants from targeted sequencing, and/or build a reference profile (link)
CuffdiffPerforms differential analysis to identify significant changes in transcript expression, splicing, and promoter use (link)
CUSHAW2 FASTA IndexerIndexes a FASTA reference genome sequence for downstream use by the CUSHAW2 mapping app (link)
CUSHAW2 FASTQ Read MapperMaps FASTQ reads (paired or unpaired) to a reference genome with the CUSHAW2 software (link)
DFilter Peak CallerCalls peaks in NGS mappings using DFilter (link)
elPrep Mark Duplicates (Intel)Marks Duplicates in a BAM File in a fast, optimized manner (link)
FastQC Reads Quality ControlGenerates a QC report on reads data (link)
File ConcatenatorConcatenates multiple files into a single one (link)
Flexbar FASTQ Read TrimmerTrims FASTQ reads by quality and/or position (link)
FreeBayes Variant CallerFreebayes calls SNPs and Indels in one or many BAM files using a Bayesian model. It performs indel realignment internally and so does not require GATK best practices. (link)
GATK-Lite Base Quality Score RecalibratorRecalibrates/improves error estimates (quality scores) of individual bases in mappings (using GATK-lite) (link)
GATK-Lite Indel RealignerRealigns mappings around indels to clean up artifacts (using GATK-lite) (link)
GATK-Lite Variant Caller (unified genotyper)Calls SNPs and/or indels (using GATK-lite Unified Genotyper) (link)
GATK3 Human Exome Pipeline(Requires a user-provided GATK 3.x jar file). Implements the GATK 3.x best practices pipeline for human exomes, including deduplicating, realigning and recalibrating mappings, and calling variants. (link)
Gzip File CompressorCompresses a file with gzip (link)
Ion Torrent TS-4.0.2 Variant CallerCalls SNPs and indels within target regions in Ion Torrent mappings, using Torrent Suite 4.0.2 software (link)
LoFreq Somatic Variant CallerCalls somatic variants using LoFreq (link)
LoFreq Variant CallerCalls variants using LoFreq (link)
Picard DownsampleSam Mappings DownsamplerRandomly downsamples a BAM file to retain a random subset of the entries (link)
Picard MarkDuplicates Mappings DeduplicatorIdentifies redundant mappings (originating from duplicate molecules) and flags or removes them (link)
Picard NormalizeFasta FASTA NormalizerNormalizes a FASTA reference genome sequence for better downstream compatibility (link)
PLINKWhole genome association analysis toolset (link)
QUASTQuality Assessment Tool for Genome Assemblies (link)
RayParallel genome assemblies for parallel DNA sequencing (link)
SAMtools Mappings IndexerCreates an index file for sorted mappings (link)
SAMtools Mappings SorterSorts mappings by coordinate (or by read name) (link)
SAMtools MD Tag GeneratorGenerates the MD tag for mappings in a BAM file using SAMtools (link)
SAMtools Variant CallerCalls SNPs and indels (using SAMtools) (link)
Swiss Army KnifeA multi-purpose tool for all your basic analysis needs (link)
TMAP BAM Read MapperMaps unmapped BAM reads (as output by Ion Torrent instruments) to a reference genome with the TMAP software (link)
TMAP FASTA IndexerIndexes a FASTA reference genome sequence for downstream use by the TMAP mapping app (link)
TopHatMaps FASTQ reads (paired or unpaired) to a reference transcriptome/genome with the TopHat 2 software (link)
Tuxedo Protocol Resource BuilderPrepares a resource archive (genome and transcriptome sequences and indices) to use with the Tuxedo protocol apps (link)
VelvetShort read de novo assembler using de Bruijn graphs (link)
Vendor Human Exome GATK-Lite PipelineCalls variants (and deduplicates, realigns and recalibrates mappings) in common vendor human exome coordinates, with GATK-lite (link)
Vendor Human Exome Selection MetricsCalculates mappings metrics for common vendor human exome kits, with Picard CalculateHsMetrics (link)

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Apps available upon request

The following apps are available as applets built by the DNAnexus team. Please contact support@dnanexus.com if you would like access to these applets

NameDescription
All-Paths
Atlas2Atlas2 calls SNP and Indels as used by Baylor College of Medicine
BreakdancerBreakdancer finds structual variants from mapped paired-end next-generation sequencing data.
CNVnatorCNVnator discovers and genotypes CNVs from read-depth analysis.
CrestCrest detects genomic structural variations at base-pair resolution
Cufflinks/CuffdiffCuffdiff finds significant changes in transcript expression, splicing, and promoter use.
DellyDelly calls SNPS and indels.
GATK-Lite UnifiedGenotyperGATK-Lite UnifiedGenotyper calls SNPs and Indels. Indel realignment and base quality score recalibration are recommended prior to calling
GATK3 BaseQualityScoreRecalibratorGATK3 BaseQualityScoreRecalibrator uses GATK3.4 to recalibrate the quality scores of Illumina reads to discover and account for inconsistencies in quality scores that may arise from factors such as cycle number, sequencing library, and sequence context
GATK3 HaplotypeCallerGATK3 HaplotypeCaller calls SNPs and Indels. HaplotypeCaller uses its own model for construction of haplotypes so indel realigner is not needed, though Broad recommends it. Base quality score recalibration is recommended.
GATK3 Indel RealignerGATK3 IndelRealigner uses GATK3.3 to realign mapped reads around potential indel sites for improved accuracy in SNP and Indel calling.
GATK3 UnifiedGenotyperGATK3 UnifiedGenotyper calls SNPs and Indels. Indel realignment and base quality score recalibration are recommended prior to calling
KallistoKallisto quantifies abundances of transcripts from RNA-Seeq data.
LumpyLumpy discovers structural variants.
MuSE
NovoalignNovocraft maps reads to a reference genome. Novocraft has a very low false mapping rate
Parliament Combine SV Calls
Parliament Local Assembly
PBHoneyPBHoney identifies structural variants using intra-read discordance and soft-clipped tails of long reads.
PindelPindel finds breakpoints for deletions, insertions, inversions, and duplications.
PlatypusPlatypus calls SNPs and Indels in one or many samples. Platypus performs internal realignment around indels, base quality score recalibration, and duplicate marking. Platypus can call indels up to 50 bp in length.
QuiverQuiver calls consensus from PacBio reads
RSEMRSEM estimates gene and isoform expression from RNA-Seq data
Samtools mpileupSamtools mpileup calls SNPs and Indels.
SNAPSNAP maps reads against a reference genome.
SOAP2SOAP2 maps reads against a reference genome.
SOAPdenovoSOAPdenovo assembles Illumina whole-genome shotgun read sets of human-scale genomes.
SOAPSNPSOAPSNP calls SNPs and Indels
Somatic SniperSomatic Sniper identifies SNPs that differ between a tumor BAM file and a normal BAM file
STARSTAR aligns RNA-Seq reads.
TMAPTMAP maps reads against a reference genome.
Varscan GermlineVarscan germline uses the non-somatic components of Varscan to call SNPs and Indels.
Varscan Somatic
XHMMXHMM detects copy number variations in whole-exome sequencing data.

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Workflows

The following workflows are available on DNAnexus. If a link is not listed and you're interested in access to the workflow, please contact support@dnanexus.com to get access.

NameDescription
Bionano GenomicsTools for de novo assembly, structural variation discovery, and hybrid scafflolding of NGS assemblies using long-range genomic information from Bionano physical genome maps. (link)
Broad Inst Viral NGSSabeti lab pipeline for assembly and analysis of Ebola, Lassa and other viral genomes (link)
BWA Whole Genome SequencingBWA/GATK Whole Genome Sequencing processes whole-genome sequencing data using BWA for alignment and variant detection using GATK. This is based on the BWA/GATK best practices workflow for GATK version 1.6.
ConiferConifer discovers disruptive genic CNVs. (contact support@dnanexus.com for access)
ENCODE Uniform Processing Pipelines: Bisulfite-SeqMap bisulfite sequencing reads to a reference genome, call CG, CHG, and CHH methylated regions, and collect quality-control metrics. (link)
ENCODE Uniform Processing Pipelines: Histone CHIP-SeqMap replicated ChIP-seq reads to a reference genome; call narrow, gapped, and broad peaks vs. controls and; compute cross-correlation and quality-control metrics. (link)
ENCODE Uniform Processing Pipelines: RNA-SeqMap short RNA reads to a reference genome, quantify transcript abundances, collect quality-control metrics, and prepare BigWig files for visualization. (link)
HGSC_MercuryMercury is a full pipeline for aligning and cleaning short read alignment data and producing variant calls on the results. Baylor College of Medicine uses this as their production pipeline for processing whole genomes and whole exomes.� (link)
PacBio FALCON AssemblerFALCON is a diploid aware whole genome assembler.� Designed for PacBio long read technology, this application takes as input fasta files and produces a set of error corrected reads, overlap files, and a set of consensus contigs making up the assembly.� This application is based upon FALCON 0.2.2 from PacBio. (link)
ParliamentParliament is a structural variant caller framework which attempts to assemble across breakpoints detected by other structural variant callers. Parliament utilizes Breakdancer, CNVnator, CREST, Delly, Pindel, and Tireisias to detect possible breakpoints but is also flexible to incorporate additional structural variation callers. Parliament then assembles across these breakpoints using both short read and long read technology. (link)
StrelkaStrelka detects somatic SNVs and small indels from sequencing data of matched tumor-normal samples. (contact support@dnanexus.com for access)

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Last edited by Phil Sung (psung), 2015-12-03 19:12:39

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