Sequence Alignment/Map format: a comprehensive review of approaches and applications
Abstract The Sequence Alignment/Map (SAM) format file is the text file used to record
alignment information. Alignment is the core of sequencing analysis, and downstream tasks …
alignment information. Alignment is the core of sequencing analysis, and downstream tasks …
Ensembl Genomes 2020—enabling non-vertebrate genomic research
KL Howe, B Contreras-Moreira, N De Silva… - Nucleic acids …, 2020 - academic.oup.com
Abstract Ensembl Genomes (http://www. ensemblgenomes. org) is an integrating resource
for genome-scale data from non-vertebrate species, complementing the resources for …
for genome-scale data from non-vertebrate species, complementing the resources for …
Sharing interoperable workflow provenance: A review of best practices and their practical application in CWLProv
Background The automation of data analysis in the form of scientific workflows has become
a widely adopted practice in many fields of research. Computationally driven data-intensive …
a widely adopted practice in many fields of research. Computationally driven data-intensive …
The Ensembl gene annotation system
The Ensembl gene annotation system has been used to annotate over 70 different
vertebrate species across a wide range of genome projects. Furthermore, it generates the …
vertebrate species across a wide range of genome projects. Furthermore, it generates the …
Sambamba: fast processing of NGS alignment formats
Sambamba is a high-performance robust tool and library for working with SAM, BAM and
CRAM sequence alignment files; the most common file formats for aligned next generation …
CRAM sequence alignment files; the most common file formats for aligned next generation …
Rfam 12.0: updates to the RNA families database
The Rfam database (available at http://rfam. xfam. org) is a collection of non-coding RNA
families represented by manually curated sequence alignments, consensus secondary …
families represented by manually curated sequence alignments, consensus secondary …
Analysis tool web services from the EMBL-EBI
Abstract Since 2004 the European Bioinformatics Institute (EMBL-EBI) has provided access
to a wide range of databases and analysis tools via Web Services interfaces. This comprises …
to a wide range of databases and analysis tools via Web Services interfaces. This comprises …
Ribosomal Database Project: data and tools for high throughput rRNA analysis
JR Cole, Q Wang, JA Fish, B Chai… - Nucleic acids …, 2014 - academic.oup.com
Abstract Ribosomal Database Project (RDP; http://rdp. cme. msu. edu/) provides the
research community with aligned and annotated rRNA gene sequence data, along with tools …
research community with aligned and annotated rRNA gene sequence data, along with tools …
GenBank
DA Benson, K Clark, I Karsch-Mizrachi… - Nucleic acids …, 2013 - pmc.ncbi.nlm.nih.gov
GenBank® is a comprehensive database that contains publicly available nucleotide
sequences for over 280 000 formally described species. These sequences are obtained …
sequences for over 280 000 formally described species. These sequences are obtained …