NGS and Long Read Sequence Assembly and Analysis Survey

Question Title

* 1. Which of the following sequencing technologies do you currently use, or plan to use, in your work?

Sanger/ABI data

Illumina

PacBio

Ion Torrent

Oxford Nanopore

Roche 454

I don't use sequencing in my work

Other (please specify)

Question Title

* 2. How likely are you to consider long read sequencing technologies, such as PacBio or Oxford Nanopore, for each of the following workflows?

	Very likely	Likely	Unlikely	Very unlikely	Unsure
Whole genome assembly	Whole genome assembly Very likely	Whole genome assembly Likely	Whole genome assembly Unlikely	Whole genome assembly Very unlikely	Whole genome assembly Unsure
Structural variant analysis	Structural variant analysis Very likely	Structural variant analysis Likely	Structural variant analysis Unlikely	Structural variant analysis Very unlikely	Structural variant analysis Unsure
RNA-Seq isoform analysis	RNA-Seq isoform analysis Very likely	RNA-Seq isoform analysis Likely	RNA-Seq isoform analysis Unlikely	RNA-Seq isoform analysis Very unlikely	RNA-Seq isoform analysis Unsure
Haplotype analysis	Haplotype analysis Very likely	Haplotype analysis Likely	Haplotype analysis Unlikely	Haplotype analysis Very unlikely	Haplotype analysis Unsure
Metagenomics	Metagenomics Very likely	Metagenomics Likely	Metagenomics Unlikely	Metagenomics Very unlikely	Metagenomics Unsure

Other (please specify)

Question Title

* 3. How important is a near perfect base sequence to you?

Not important

Hope software will automatically produce a perfect sequence for me

Willing to do some post-assembly editing to improve the sequence

Critical. Will do whatever post-assembly editing is necessary for a near perfect sequence

Question Title

* 4. How important is a closed genome to you?

Not important

Hope software will automatically close it for me

Willing to do some post-assembly finishing to close

Critical. Will do whatever post-assembly finishing is necessary

Question Title

* 5. Do you need to annotate genomes?

Yes

Not now, but in the future

Question Title

* 6. Given the recent advances in targeting genomic regions of interest for long read sequencing, how likely are you to try any of those technologies?

Very likely

Likely

Unlikely

Very unlikely

Unsure

Question Title

* 7. Where do you think long read technology can provide the most value in your lab?

Cost

Ability to sequence through repeat regions

Accuracy

Ability to scale

None of the above

Other (please specify)

Question Title

* 8. What, if any, of the following factors would prevent you from using long read sequencing?

Cost

Access to reagents or instruments

Availability of data analysis tools

Sequencing error rate

None

Other (please specify)

Question Title

* 9. What tools do you use for NGS assembly or analysis? Check all that apply

Lasergene/SeqMan NGen

CLC Genomics Workbench

Geneious

Galaxy

BioConductor

None

Other (please specify)

Question Title

* 10. What tools do you use for long read sequencing assembly or analysis? Check all that apply.

Canu/Pilon

Unicycler/SPAdes

HGAP

ALLPATHS-LG

None

Other (please specify)

Question Title

* 11. How satisfied are you with the tools you currently use for Sanger, NGS and/or long read assembly, alignment and analysis?

Very satisfied

Satisfied

Dissatisfied

Very dissatisfied

N/A

Question Title

* 12. Considering all the software you use for NGS and long read analysis, what are the biggest areas for improvement? Select up to 3 options.

UX/Usability

Software support

Speed

Accuracy

Support for different data types

Ability to edit and share files

Other (please specify)

Question Title

* 13. Would you be willing to try a new assembly and/or analysis program?

Yes

Unsure

Question Title

* 14. What factors would most influence your decision to change assembly or analysis tools? Choose up to 3.

Accuracy of results

Ease of use

Ability to perform a variety of workflows

Support for the latest sequencing technologies

Technical support

A complete pipeline from read assembly to analysis

Ability to perform specific analysis tool or method (please elaborate in comments)

Other (please specify)

Question Title

* 15. Would you like to be contacted about a beta test or customer preview of a new long read assembly application?

Yes

NGS and Long Read Sequence Assembly and Analysis

Long Read Sequencing and Genomic Assembly in Your Research

Question Title

* 1. Which of the following sequencing technologies do you currently use, or plan to use, in your work?

Question Title

* 2. How likely are you to consider long read sequencing technologies, such as PacBio or Oxford Nanopore, for each of the following workflows?

Question Title

* 3. How important is a near perfect base sequence to you?

Question Title

* 4. How important is a closed genome to you?

Question Title

* 5. Do you need to annotate genomes?

Question Title

* 6. Given the recent advances in targeting genomic regions of interest for long read sequencing, how likely are you to try any of those technologies?

Question Title

* 7. Where do you think long read technology can provide the most value in your lab?

Question Title

* 8. What, if any, of the following factors would prevent you from using long read sequencing?

Question Title

* 9. What tools do you use for NGS assembly or analysis? Check all that apply

Question Title

* 10. What tools do you use for long read sequencing assembly or analysis? Check all that apply.

Question Title

* 11. How satisfied are you with the tools you currently use for Sanger, NGS and/or long read assembly, alignment and analysis?

Question Title

* 12. Considering all the software you use for NGS and long read analysis, what are the biggest areas for improvement? Select up to 3 options.

Question Title

* 13. Would you be willing to try a new assembly and/or analysis program?

Question Title

* 14. What factors would most influence your decision to change assembly or analysis tools? Choose up to 3.

Question Title

* 15. Would you like to be contacted about a beta test or customer preview of a new long read assembly application?

Question Title

* 16. Contact Details

Question Title

* 17. Is there anything else you'd like to share? (Optional)