Bioinformatics

• Team consultation
• Experimental design
• Variety of computational and bioinformatics analyses
• Training on specific analysis upon request
• Customized analysis pipelines

Microbiome 16S/18S/ITS Sequencing Data Analysis

• Type of Data: Targeted sequencing of any of the 16S or 18S or ITS regions.
• Analysis methods: 
  Quality-based sequence trimming and removal of adapters and specific primer sequences, removal of chimeric sequences, joining the forward and reverse reads, representative sequences identification, taxonomy classification, and statistical analysis.
• Deliverables: 
  Species Richness per sample, Species Relative Abundance among samples, Core Microbiomes, Alpha-diversity, Beta-diversity, Differential Analysis

 RNA-Seq

• Type of Data:  Illumina PE 50, 75, 100, etc… stranded libraries.  Required: annotated (GFF3/GTF) genome or transcriptome.
• Analysis methods: 
  Data Quality Assessment (Raw and Trimmed): FastQC
  Data Quality Trimming: Trimmomatic
  Mapping:  STAR/Bowtie2, depending on input dataset.
  Expression Analysis: DESeq2/edgeR/RSEM, depending on reference and 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.

Small RNA (sRNA) 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.

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.

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).

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).

Eukaryotic Genome Assembly (de novo, long 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).

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.

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.

Single-cell RNA-Seq Data Analysis

• Type of Data: 10x Single-cell RNA-sequencing Data
• Analysis methods: 
  Data Quality Control
  Data processing: Normalization, Principal component analysis (PCA) dimension reduction, Clustering/Community Detection.
  Data visualization: t-Distributed Stochastic Neighbor Embedding (t-SNE)/ Uniform
  Manifold Approximation and Projection (UMAP) cell visualization.
  Cell Trajectories analysis, Pseudo-time analysis, Differential expression analysis, Single-cell time series analysis
• Deliverables:
  Comprehensive Report on all requested analysis including codes, figures and paper format writing explanations.

Analysis on CRISPR Genetic screens

• Type of Data: Genome-wide screen data
• Analysis methods: 
  Generating the raw count table using “MAGeCK” MAGeCK raw count and Batch effect remove. MAGeCK raw count and NO Batch remove. MAGeCK raw count and DEseq2 package analysis.
• Deliverables:
  Comprehensive Report on all requested analysis including codes, figures and paper format writing explanations.

Circular Consensus Sequencing (CCS) Read Generation

• Type of Data: PacBio Sequel II
• Analysis methods: 
  Generation of CCS reads resulting from alignment between subreads taken from a single ZMW.  CCS reads are advantageous for amplicon, RNA, and genome sequencing projects and are highly accurate (>99% accuracy, Q>20).
• Deliverables:
  A CCS.bam file for each SMRT cell run and a text file containing read generation statistics and metrics.

Service	UGA Fee	Non-UGA Fee	Commercial Fee
De novo transcriptome assembly from illumina short reads	$1,500	$1,770	$1,875
De novo transcriptome assembly from PacBio Iso-Seq data	$1,500	$1,770	$1,875
Assembly of small (< 50 Mb) eukaryotic genomes	custom	custom	custom
Microbial genome assembly & annotation (1-2 genomes) from PacBio long reads	$1,000	$1,180	$1,250
Microbial genome assembly & annotation (3-5 genomes) from PacBio long reads	$1,500	$1,770	$1,875
Microbial genome assembly & annotation (6-10 genomes) from PacBio long reads	$2,000	$2,360	$2,500
Bacterial draft genome: sequencing using Illumina short reads/assembly/annotation	$1,000	$1,180	$1,250
Transcriptome annotation (basic)	$500	$590	$625
RNA-Seq or sRNA-Seq analysis (up to 24 samples, single mapping reference)	$1,500	$1,770	$1,875
RNA-Seq or sRNA-Seq analysis (25 to 72 samples, single mapping reference)	$2,000	$2,360	$2,500
RNA-Seq or sRNA-Seq analysis (above 73 to 96 samples, single mapping reference)	$2,500	$2,950	$3,125
RNAseq or sRNAseq analysis (for each additional mapping reference)	$500	$590	$625
Single Cell RNA-Seq analysis	$1,000	$1,180	$1,250
GO tag and InterProScan annotation	$300	$354	$375
SNPs detection/calling/filtering (up to 24 samples)	$1,500	$1,770	$1,875
GBS analysis using STACKS (up to 96 samples)	$1,500	$1,770	$1,875
Microbiome analysis (up to 24 samples)	$500	$590	$625
Microbiome analysis (25-96 samples)	$1,000	$1,180	$1,250
Bacterial genome submission to NCBI	$250	$295	$313
PacBio: CCS reads generation	$300	$354	$375
Hourly rate for custom jobs and/or personnel training	$75	$89	$94

 

Please contact GGBC to inquire about pricing for any bioinformatics services not listed above.

10X Single Cell Data Demultiplexing Tutorial

Illumina Data Demultiplexing Tutorial

Illumina Data Assessment and Trimming