Genome browsers are useful not only for showing final results but also for improving analysis protocols, testing data quality, and generating result drafts. Its integration in analysis pipelines allows the optimization of parameters, which...
Global overview papers
Next generation quantitative genetics in plants. Jiménez-Gómez, Frontiers in Plant Science 2:77, 2011 Full Text [equally relevant to animal and microbial systems]
Sense from sequence reads: methods for...
www.h-invitational.jp - G-compass (http://www.h-invitational.jp/g-compass/) is a comparative genome browser. It visualizes evolutionarily conserved genomic regions between human and other 12 vertebrates based on original genome alignments pursuing higher coverage (1,2)....
www.rdatamining.com - This website presents examples, documents and resources on data mining with R. Documents on using R for data mining are available to download for non-commercial personal use, including R Reference card for Data Mining, R and Data Mining:...
www.fishbrowser.org - P_RNA_scaffolder, a fast and accurate tool using paired-end RNA-sequencing reads to scaffold genomes. This tool aims to improve the completeness of both protein-coding and non-coding genes. After this tool was applied to scaffolding human contigs,...
Awk is a programming language that is specifically designed for quickly manipulating space delimited data. Although you can achieve all its functionality with Perl, awk is simpler in many practical cases.
Why awk? You can replace a pipeline...
National Institute for Research in Reproductive Health
(Indian Council of Medical Research )
Jehangir Merwanji Street, Parel, Mumbai 400 012
Advertisement No. 1/NIRRH/Ph.D. 2013
Admission to Ph.D. Programme – 2013
National Institute for...
FYI, I've found it useful to use MUMmer to extract the specific changes that Racon makes, so I can evaluate them individually:
minimap -t 24 assembly.fasta long_reads.fastq.gz | racon -t 24 long_reads.fastq.gz - assembly.fasta...
The Computational Biology research group was established in October 2012 at the Department of Mathematics and Computer Science (IMADA) at the University of Southern Denmark (SDU). It emerged from the Computational Systems Biology group, founded in...
chmille4.github.io - Scribl is a javascript, Canvas-based graphics library that easily generates biological visuals of genomic regions, alignments, and assembly data. Scribl can also be used in conventional offline pipelines, since everything needed to generate charts...