Visitors   Views   Downloads

SECAPR - A bioinformatics pipeline for the rapid and user-friendly processing of Illumina sequences, from raw reads to alignments

View preprint
RT @Alex_deMenezes: Bioinformatic pipeline to work with hybrid Illumina sequence capture enrichments https://t.co/QEkRu0kkpR
Bioinformatic pipeline to work with hybrid Illumina sequence capture enrichments https://t.co/QEkRu0kkpR
SECAPR pipeline for aligning FASTQ data https://t.co/Tism0BJJRe via @PeerJPreprints
290 days ago
SECAPR - A bioinformatics pipeline for the rapid and user-friendly alignment of hybrid enrichment sequences, from raw reads to alignments https://t.co/8WCZk43ynl
NOT PEER-REVIEWED
"PeerJ Preprints" is a venue for early communication or feedback before peer review. Data may be preliminary.

A peer-reviewed article of this Preprint also exists.

View peer-reviewed version

Supplemental Information

Appendix 1: Library preparation and sequencing of Geonoma sample data

Detailed description of the lab workflow.

DOI: 10.7287/peerj.preprints.26477v3/supp-1

Table S1: Biological data info

Reported are the IDs of the Geonoma sample data and the locality and collector information about each sample.

DOI: 10.7287/peerj.preprints.26477v3/supp-2

Table S2: Overview of recovered contigs

The table shows which exon locus had a matchign contig in each of the Geonoma samples.

DOI: 10.7287/peerj.preprints.26477v3/supp-3

Table S3: Overview of all contigs flagged by the find_traget_contigs function

The document contains a list of all contigs that were flagged by the find_target_contigs function. Listed for each sample are all exons which were excluded because of possible paralogy (more than one matching contig). Further for each sample are listed all contig IDs, which matched multiple exons, which we did not exclude in the example data, as they were mostly representing long contigs spanning across several adjacent exons.

DOI: 10.7287/peerj.preprints.26477v3/supp-4

Table S4: Overview of read-coverage for selected exon loci

The table contains an overview of the read-depth information for all 97 exon loci that had an average read-depth of at least 3 reads across all Geonoma samples.

DOI: 10.7287/peerj.preprints.26477v3/supp-5

Table S5: Exon index legend for Fig. 4

This table contains an overview of which exon locus corresponds to which index in Fig. 4 of the manuscript.

DOI: 10.7287/peerj.preprints.26477v3/supp-6

Additional Information

Competing Interests

The authors declare that they have no competing interests.

Author Contributions

Tobias Andermann conceived and designed the experiments, analyzed the data, contributed reagents/materials/analysis tools, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.

Angela Cano contributed reagents/materials/analysis tools, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft, reviewed the manuscript.

Alexander Zizka contributed reagents/materials/analysis tools, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft, reviewed the manuscript.

Christine Bacon conceived and designed the experiments, authored or reviewed drafts of the paper, approved the final draft, reviewed the manuscript.

Alexandre Antonelli conceived and designed the experiments, authored or reviewed drafts of the paper, approved the final draft, reviewed the manuscript.

DNA Deposition

The following information was supplied regarding the deposition of DNA sequences:

The raw FASTQ sequences of the Geonoma sample data are available at the NCBI Short Read Archive (SRA) via accession number SRP131660: https://www.ncbi.nlm.nih.gov/sra/SRP131660

Data Deposition

The following information was supplied regarding data availability:

All files resulting from processing of the Geonoma sample data are deposited at Zenodo under https://doi.org/10.5281/zenodo.1162653

Funding

This work was supported by the Swedish Research Council (B0569601), the European Research Council under the European Union’s Seventh Framework Programme (FP/2007-2013, ERC Grant Agreement n. 331024), the Swedish Foundation for Strategic Research, the Faculty of Science at the University of Gothenburg, the David Rockefeller Center for Latin American Studies at Harvard University, and a Wallenberg Academy Fellowship to Alexandre Antonelli; and a SciLifeLab Bioinformatics Long-term Support from the Wallenberg Advanced Bioinformatics Infrastructure to Alexandre Antonelli and Bengt Oxelman. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.


Add your feedback

Before adding feedback, consider if it can be asked as a question instead, and if so then use the Question tab. Pointing out typos is fine, but authors are encouraged to accept only substantially helpful feedback.

Some Markdown syntax is allowed: _italic_ **bold** ^superscript^ ~subscript~ %%blockquote%% [link text](link URL)
 
By posting this you agree to PeerJ's commenting policies