publication . Article . Other literature type . Preprint . 2019

Alvis: a tool for contig and read ALignment VISualisation and chimera detection

Samuel Martin; Richard Leggett;
Open Access English
  • Published: 06 Jun 2019 Journal: BMC Bioinformatics, volume 22, issue 1, pages 1-10 (issn: 1471-2105, Copyright policy)
  • Publisher: BMC
Abstract
<jats:title>Abstract</jats:title><jats:sec> <jats:title>Background</jats:title> <jats:p>The analysis of long reads or the assessment of assembly or target capture data often necessitates running alignments against reference genomes or gene sets. The aligner outputs are often parsed automatically by scripts, but many kinds of analysis can benefit from the understanding that can follow human inspection of individual alignments. Additionally, diagrams are a useful means of communicating assembly results to others.</jats:p> </jats:sec><jats:sec> <jats:title>Results</jats:title> <jats:p>We developed Alvis, a simple command line tool that can generate visualisations f...
Subjects
free text keywords: Sequence alignment, Genomics, Visualisation, Chimera detection, Biochemistry, Applied Mathematics, Molecular Biology, Structural Biology, Computer Science Applications, Software, lcsh:Computer applications to medicine. Medical informatics, lcsh:R858-859.7, lcsh:Biology (General), lcsh:QH301-705.5, Vector graphics, Correctness, Visualization, Scripting language, computer.software_genre, computer, Artificial intelligence, business.industry, business, Parsing, Computer science, Contiguity, Natural language processing, Target capture, Contig
Related Organizations
Communities
Digital Humanities and Cultural Heritage
Download fromView all 5 versions
BMC Bioinformatics
Article . 2021
Provider: Crossref
bioRxiv
Preprint . 2019
Provider: bioRxiv

1. Zerbino DR, Achuthan P, et al. Ensembl 2018. Nucleic Acids Research 2018;46:754-761.

2. Robinson JT, Thorvaldsdóttir H, et al. Integrative Genomics Viewer. Nature Biotechnology 2011;29:24-26.

3. Krzywinski M, et al. Circos: an information aesthetic for comparative genomics. Genome Research 2009;19:1639- 1645. [OpenAIRE]

4. Schnable PS, et al. The B73 Maize Genome: Complexity, Diversity and Dynamics. Science 2009;326:1112-1115.

5. Kurtz S, Phillippy A, Delcher AL, et al. Versatile and open software for comparing large genomes. Genome Biology 2004;5(2):12. [OpenAIRE]

6. Boratyn GM, Camacho C, Cooper PS, et al. BLAST: a more e cient report with usability improvements. Nucleic Acids Research 2013;41:29-33. [OpenAIRE]

7. Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics 2009;25:1754-1756.

8. Li H. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics 2018;34(18):3094-3100.

9. Kent JW. BLAT - The BLAST-Like Alignment Tool. Genome Research 2002;12(4):656-66.

10. Jupe F, et al. Resistance gene enrichment sequencing (RenSeq) enables reannotation of the NB-LRR gene family from sequenced plant genomes and rapid mapping of resistance loci in segregating populations. The Plant Journal 2013;76(3):530-544. [OpenAIRE]

11. Michael TP, Jupe F, Bemm F, et al. High contiguity Arabidopsis thaliana genome assembly with a single nanopore ow cell. Nature Communications 2018;9.

12. Jain M, Koren S, et al. Nanopore sequencing and assembly of a human genome with ultra-long reads. Nature Biotechnology 2018;36:338-345.

13. Lamesch P, Berardini TZ, Donghui L, Swarbreck D, et al. The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools. Nucleic Acids Research 2012;40(Database issue):D1202-D1210. [OpenAIRE]

14. Schneider VA, Graves-Lindsay T, Howe K, et al. Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly. bioRxiv 2016;.

15. Kolmogorov M, Yuan J, Lin Y, Pevzner P. Assembly of Long Error-Prone Reads Using Repeat Graphs. bioRxiv 2018;. [OpenAIRE]

Related research
Abstract
<jats:title>Abstract</jats:title><jats:sec> <jats:title>Background</jats:title> <jats:p>The analysis of long reads or the assessment of assembly or target capture data often necessitates running alignments against reference genomes or gene sets. The aligner outputs are often parsed automatically by scripts, but many kinds of analysis can benefit from the understanding that can follow human inspection of individual alignments. Additionally, diagrams are a useful means of communicating assembly results to others.</jats:p> </jats:sec><jats:sec> <jats:title>Results</jats:title> <jats:p>We developed Alvis, a simple command line tool that can generate visualisations f...
Subjects
free text keywords: Sequence alignment, Genomics, Visualisation, Chimera detection, Biochemistry, Applied Mathematics, Molecular Biology, Structural Biology, Computer Science Applications, Software, lcsh:Computer applications to medicine. Medical informatics, lcsh:R858-859.7, lcsh:Biology (General), lcsh:QH301-705.5, Vector graphics, Correctness, Visualization, Scripting language, computer.software_genre, computer, Artificial intelligence, business.industry, business, Parsing, Computer science, Contiguity, Natural language processing, Target capture, Contig
Related Organizations
Communities
Digital Humanities and Cultural Heritage
Download fromView all 5 versions
BMC Bioinformatics
Article . 2021
Provider: Crossref
bioRxiv
Preprint . 2019
Provider: bioRxiv

1. Zerbino DR, Achuthan P, et al. Ensembl 2018. Nucleic Acids Research 2018;46:754-761.

2. Robinson JT, Thorvaldsdóttir H, et al. Integrative Genomics Viewer. Nature Biotechnology 2011;29:24-26.

3. Krzywinski M, et al. Circos: an information aesthetic for comparative genomics. Genome Research 2009;19:1639- 1645. [OpenAIRE]

4. Schnable PS, et al. The B73 Maize Genome: Complexity, Diversity and Dynamics. Science 2009;326:1112-1115.

5. Kurtz S, Phillippy A, Delcher AL, et al. Versatile and open software for comparing large genomes. Genome Biology 2004;5(2):12. [OpenAIRE]

6. Boratyn GM, Camacho C, Cooper PS, et al. BLAST: a more e cient report with usability improvements. Nucleic Acids Research 2013;41:29-33. [OpenAIRE]

7. Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics 2009;25:1754-1756.

8. Li H. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics 2018;34(18):3094-3100.

9. Kent JW. BLAT - The BLAST-Like Alignment Tool. Genome Research 2002;12(4):656-66.

10. Jupe F, et al. Resistance gene enrichment sequencing (RenSeq) enables reannotation of the NB-LRR gene family from sequenced plant genomes and rapid mapping of resistance loci in segregating populations. The Plant Journal 2013;76(3):530-544. [OpenAIRE]

11. Michael TP, Jupe F, Bemm F, et al. High contiguity Arabidopsis thaliana genome assembly with a single nanopore ow cell. Nature Communications 2018;9.

12. Jain M, Koren S, et al. Nanopore sequencing and assembly of a human genome with ultra-long reads. Nature Biotechnology 2018;36:338-345.

13. Lamesch P, Berardini TZ, Donghui L, Swarbreck D, et al. The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools. Nucleic Acids Research 2012;40(Database issue):D1202-D1210. [OpenAIRE]

14. Schneider VA, Graves-Lindsay T, Howe K, et al. Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly. bioRxiv 2016;.

15. Kolmogorov M, Yuan J, Lin Y, Pevzner P. Assembly of Long Error-Prone Reads Using Repeat Graphs. bioRxiv 2018;. [OpenAIRE]

Related research
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