Bioinformatics

 

GGBC provides a wide range of bioinformatics services. The analysis workflow has been divided into basic modules. This approach allows customers to purchase only the services they need. It also creates very clear deliverables for each step in the analysis.

Services
  • Team consultation: Prior to grants and experiments (2 hours free)
  • Tutorial: Module-based tutoring sessions
  • A la carte: Order specific analysis workflow or modules
Bioinformatics workflow
  • Experimental design
  • Data suitability assessment
  • Quality and variables assessment
  • Reference assessment and preparation
  • Analysis workflows
  • Training in how to perform the above steps (if desired)
Guidelines for Different Analysis Workflows

Analysis name: RNA-Seq

  • Type of Data:  Illumina PE 75, stranded library.  Required: annotated (GFF3/GTF) genome or transcriptome.
  • Analysis methods: 
    Data Quality Assessment (Raw and Trimmed): FastQC
    Data Trimming: Trimmomatic
    Mapping:  Bowtie2/Tophat/RSEM, depending on input dataset.
    Expression Analysis: Cuffdiff/DESeq2/edgR, depending on dataset.
  • Deliverables: 
    Quality assessment for all samples (raw and trimmed), PCA and/or BCV analysis of samples, MA plots, list of differentially expressed genes in Excel format including fold change, P values, FDR, normalized counts, etc… as well as ancillary files, e.g. read mapping metrics, BAM files.

Analysis name: microRNA Expression Analysis

  • Type of Data:  Illumina SE75 (CAP-miRSeq requirements: reference genome, miRbase species accession)
  • Analysis methods:
    Data Quality Assessment (Raw and Trimmed): FastQC
    Data Trimming: CutAdapt
    Expression Analysis: CAP-miRSeq Pipeline (Bowtie, Randfold, HTSEQ, MIRDEEP2)
  • Deliverables:
    Quality assessment for all samples (raw and trimmed), trimmed read distributions, profile of all small RNAs present in each sample, prediction of novel miRNAs.
    General expression results: Excel files with mature, raw, normalized and novel miRNA counts.List of differentially expressed miRNAs in Excel format including fold change, P values, FDR, normalized counts.

Analysis name: SNP Analysis

  • Type of Data:  Illumina PE75.  Mapping reference required.
  • Analysis methods: 
    Data Quality Assessment (Raw and Trimmed): FastQ Data Trimming: Trimmomatic
    Mapping and mark duplicates:  BWA, Picard
    Variant Calling and filtering: GATK
  • Deliverables:
    Quality assessment for all samples (raw and trimmed), trimmed read metrics, mapping and read duplication stats, SNP and Indel variant call files (VCF) for both raw and filtered datasets.

Analysis name: Bacterial Genome Assembly & Annotation (short read)

  • Type of Data:  Illumina PE150, PE300
  • Analysis methods: 
    Data Quality Assessment (Raw and Trimmed): FastQC
    Data Trimming: Trimmomatic
    Assembly: SPAdes
    Benchmarking: Quast, BUSCO, BlastN, Mauve
    Automated Annotation & prophage discovery: RASTtk, PHASTER
  • Deliverables:
    Assembly fasta file, Quality assessments for all samples (raw and trimmed,  Quast summary metrics (plus/minus reference), BUSCO identification of core gene set, Mauve alignment to closest genome reference and ordering of contigs, BlastN (tabular output), RASTtk annotation (xls, gff, gbk, peptide.fa), PHASTER identification of prophage sequence(s).

Analysis name: Bacterial Genome Assembly & Annotation (long read)

  • Type of Data:  PacBio
  • Analysis methods: 
    Error correction, assembly and contig polishing: Canu, BLASR, Arrow
    Benchmarking: Quast, BUSCO.
  • Deliverables:
    Assembly fasta file, Contig coverage plots, Quast summary metrics (plus/minus reference), BUSCO identification of core gene set, Mauve alignment to closest genome reference and ordering of contigs, BlastN (tabular output), RASTtk annotation (xls, gff, gbk), PHASTER identification of prophage sequence(s).

Analysis name: Eukaryotic Genome Assembly (de novo, long read)/Custom

  • Type of Data:  PacBio
  • Analysis methods:
    Error correction, assembly and contig polishing: Canu, BLASR, Arrow
    Benchmarking: Quast, BUSCO, BlastN
  • Deliverables:
    Assembly fasta file, Contig coverage plots, Quast summary metrics (plus/minus reference), BUSCO identification of core gene set, BlastN (tabular output), BLASR BAM files.

Analysis name: Eukaryotic Genome Assembly (de novo, short read)/Custom

  • Type of Data:  Illumina PE
  • Analysis methods: 
    Data Quality Assessment (Raw and Trimmed): FastQC
    Data Trimming: Trimmomatic
    Assembly: Velvet/Soapdenovo2/ABySS (depending on dataset)
    Benchmarking: Quast, BUSCO, BlastN
  • Deliverables:
    Assembly fasta file, Quast summary metrics (plus/minus reference), BUSCO identification of core gene set, BlastN (tabular output).

Analysis name: Transcriptome Assembly (short read)

  • Type of Data: PE75, PE150
  • Analysis methods: 
    Data Quality Assessment (Raw and Trimmed): FastQC
    Data Trimming: Trimmomatic
    Assembly: Trinity
    Benchmarking: Quast, BUSCO
  • Deliverables:
    Assembly fasta file, Quast summary metrics (plus/minus reference), BUSCO identification of core gene set.

Analysis name: Transcriptome Assembly (long read)

  • Type of Data: PacBio
  • Analysis methods: 
    Error Correction, assembly and contig polishing: IsoSeq3
    Transcript clustering: Minimap2, Cupcake (+ reference genome), Cogent (-/+ reference genome)
    Benchmarking: Quast, BUSCO
  • Deliverables:
    High quality and low quality fasta and fastq transcript files, locus collapsed and 5’ degradation filtered assembly fastas and gff file. Quast summary metrics (plus/minus reference), BUSCO identification of core gene set.
Prices
Service UGA FeeNon-UGA FeeCommercial Fee
De novo transcriptome assembly from illumina short reads$1,500$1,770$2,250
De novo transcriptome assembly from PacBio Iso-Seq data$1,500$1,770$2,250
Assembly and annotation of mid-sized genomes from PacBio long reads $3,500$4,130$5,250
Assembly and annotation of 1-10 bacterial genomes from PacBio long reads$2,000$2,360$3,000
Bacterial draft genome: sequencing using Illumina short reads/assembly/annotation$1,000$1,180$1,500
Transcriptome annotation (basic)$500$590$750
Differential expression analysis (up to 24 samples)$2,000$2,360$3,000
Small RNA analysis (up to 24 samples)$2,000$2,360$3,000
GO tag and InterProScan annotation$300$354$450
SNPs detection/calling/filtering$500$590$750
GBS analysis using STACKS (up to 96 samples)$1,500$1,770$2,250
Microbiome analysis (up to 12 samples) [$25 for each additional sample]$350$413$525
Bacterial genome submission to NCBI$250$295$375
Hourly rate for custom jobs and/or personnel training$75$89$113

 

We have many more analyses available. Please contact us for more information.

Rates effective 1/1/2018.