Review of alignment and SNP calling algorithms for next-generation sequencing data

M Mielczarek, J Szyda - Journal of applied genetics, 2016 - Springer
Application of the massive parallel sequencing technology has become one of the most
important issues in life sciences. Therefore, it was crucial to develop bioinformatics tools for …

[HTML][HTML] Computational tools for viral metagenomics and their application in clinical research

L Fancello, D Raoult, C Desnues - Virology, 2012 - Elsevier
There are 100 times more virions than eukaryotic cells in a healthy human body. The
characterization of human-associated viral communities in a non-pathological state and the …

snakePipes: facilitating flexible, scalable and integrative epigenomic analysis

V Bhardwaj, S Heyne, K Sikora, L Rabbani… - …, 2019 - academic.oup.com
Due to the rapidly increasing scale and diversity of epigenomic data, modular and scalable
analysis workflows are of wide interest. Here we present snakePipes, a workflow package …

Metagenomics using next-generation sequencing

L Bragg, GW Tyson - Environmental microbiology: methods and protocols, 2014 - Springer
Traditionally, microbial genome sequencing has been restricted to the small number of
species that can be grown in pure culture [1]. The progressive development of culture …

SeqMule: automated pipeline for analysis of human exome/genome sequencing data

Y Guo, X Ding, Y Shen, GJ Lyon, K Wang - Scientific reports, 2015 - nature.com
Next-generation sequencing (NGS) technology has greatly helped us identify disease-
contributory variants for Mendelian diseases. However, users are often faced with issues …

Identification of genes involved in biosynthesis of mannan polysaccharides in Dendrobium officinale by RNA-seq analysis

C He, J Zhang, X Liu, S Zeng, K Wu, Z Yu, X Wang… - Plant Molecular …, 2015 - Springer
Dendrobium officinale is a traditional Chinese medicinal plant. The stems of D. officinale
contain mannan polysaccharides, which are promising bioactive polysaccharides for use as …

Transcriptome sequencing for SNP discovery across Cucumis melo

J Blanca, C Esteras, P Ziarsolo, D Pérez… - BMC genomics, 2012 - Springer
Abstract Background Melon (Cucumis melo L.) is a highly diverse species that is cultivated
worldwide. Recent advances in massively parallel sequencing have begun to allow the …

Genome sequence and description of the mosquitocidal and heavy metal tolerant strain Lysinibacillus sphaericus CBAM5

TD Peña-Montenegro, L Lozano, J Dussán - Standards in genomic …, 2015 - Springer
Lysinibacillus sphaericus CBAM5, was isolated from subsurface soil of oil well explorations
in the Easter Planes of Colombia. This strain has potential in bioremediation of heavy-metal …

The transcriptome of Spodoptera exigua larvae exposed to different types of microbes

L Pascual, AK Jakubowska, JM Blanca… - Insect biochemistry and …, 2012 - Elsevier
We have obtained and characterized the transcriptome of Spodoptera exigua larvae with
special emphasis on pathogen-induced genes. In order to obtain a highly representative …

A primer on metagenomics and next‐generation sequencing in fish gut microbiome research

TK Johny, RM Puthusseri, SG Bhat - Aquaculture Research, 2021 - Wiley Online Library
The fish gut is a complex ecosystem populated by an exceedingly diverse and assorted
group of microbes, influenced by various factors such as habitat salinity, temperature, trophic …