Using Git has the added benefit of services like GitHub and GitLab which
facilitate collaboration with others.
5 Sequencing, Assembly, and Annotation of Genomes
De Novo
5.1 The Human Genome Project (HGP) Sets the Stage
for Plant Genome Sequencing
The HGP spurred many advances in technology and led to the development of a
number of protocols that were critical in de novo sequencing and assembly of the
first plant genome sequences. Specifically, the HGP spurred:
• The development and use of BACs as cloning vectors (along with the eventual
abandonment of yeast artificial chromosomes or YACs) – While YACs could
Table 2 (continued)
Program name hyperlinked to program download site – description (reference)
Quack – very fast and scalable quality assurance tool for evaluating FASTQ (high-throughput
sequence) files (Thrash et al. 2018)
a
Quast – evaluation of genome assemblies (Gurevich et al. 2013)
Racon – ultrafast consensus module for raw de novo genome assembly of long uncorrected reads
(Vaser et al. 2017)
RAxML – tool for maximum likelihood-based phylogenetic inference (Stamatakis 2006)
Recon – a package for automated de novo identification of repeat families from genomic
sequences (Bao and Eddy 2002)
RepeatMasker – a program that screens DNA sequences for interspersed repeats and
low-complexity DNA sequences (Smit et al. 2013)
RepeatModeler – a de novo repeat family identification and modeling package
RepeatScout – a tool to discover repetitive substrings in DNA (Price et al. 2005)
REVIGO – summarizes and visualizes long lists of Gene Ontology terms (Supek et al. 2011)
Salmon – quantify the expression of transcripts using RNA-Seq data (Patro et al. 2017)
Samtools – a suite of programs for interacting with high-throughput sequencing data (Li et al.
2009)
SNAP – SNAP is a general purpose gene-finding program suitable for both eukaryotic and
prokaryotic genomes (Zaharia et al. 2011)
StringTie – a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts
(Pertea et al. 2015)
Trimmomatic – performs a variety of useful trimming tasks for Illumina paired-end and singleended data (Bolger et al. 2014b)
Trinity – efficient and robust de novo reconstruction of transcriptomes from RNA-Seq data (Haas
et al. 2013)
a Developed at the IGBB or in collaboration with the IGBB
Sequencing Plant Genomes
151
facilitate collaboration with others.
5 Sequencing, Assembly, and Annotation of Genomes
De Novo
5.1 The Human Genome Project (HGP) Sets the Stage
for Plant Genome Sequencing
The HGP spurred many advances in technology and led to the development of a
number of protocols that were critical in de novo sequencing and assembly of the
first plant genome sequences. Specifically, the HGP spurred:
• The development and use of BACs as cloning vectors (along with the eventual
abandonment of yeast artificial chromosomes or YACs) – While YACs could
Table 2 (continued)
Program name hyperlinked to program download site – description (reference)
Quack – very fast and scalable quality assurance tool for evaluating FASTQ (high-throughput
sequence) files (Thrash et al. 2018)
a
Quast – evaluation of genome assemblies (Gurevich et al. 2013)
Racon – ultrafast consensus module for raw de novo genome assembly of long uncorrected reads
(Vaser et al. 2017)
RAxML – tool for maximum likelihood-based phylogenetic inference (Stamatakis 2006)
Recon – a package for automated de novo identification of repeat families from genomic
sequences (Bao and Eddy 2002)
RepeatMasker – a program that screens DNA sequences for interspersed repeats and
low-complexity DNA sequences (Smit et al. 2013)
RepeatModeler – a de novo repeat family identification and modeling package
RepeatScout – a tool to discover repetitive substrings in DNA (Price et al. 2005)
REVIGO – summarizes and visualizes long lists of Gene Ontology terms (Supek et al. 2011)
Salmon – quantify the expression of transcripts using RNA-Seq data (Patro et al. 2017)
Samtools – a suite of programs for interacting with high-throughput sequencing data (Li et al.
2009)
SNAP – SNAP is a general purpose gene-finding program suitable for both eukaryotic and
prokaryotic genomes (Zaharia et al. 2011)
StringTie – a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts
(Pertea et al. 2015)
Trimmomatic – performs a variety of useful trimming tasks for Illumina paired-end and singleended data (Bolger et al. 2014b)
Trinity – efficient and robust de novo reconstruction of transcriptomes from RNA-Seq data (Haas
et al. 2013)
a Developed at the IGBB or in collaboration with the IGBB
Sequencing Plant Genomes
151