BOL

Awk is a programming language which allows easy manipulation of structured data and is mostly used for pattern scanning and processing. It searches one or more files to see if they contain lines that match with the specified patterns and then...

Bioinformatics resources https://github.com/danielecook/Awesome-Bioinformatics #Bioinformatics #Resources

Important #NGS tutorial http://userweb.eng.gla.ac.uk/umer.ijaz/bioinformatics/linux.html

The purpose of this cheat sheet is to introduce biologist and bioinformatician to the frequently used tools for NGS analysis as well as giving experience in writing one-liners. File System ls — list items in current directory ls...

urbe@urbo214b[allONT] minimap2 -xava-ont both.fastq both.fastq -t20 -X > AONT.paf [][M::mm_idx_gen::107.693*1.96] collected minimizers[M::mm_idx_gen::117.963*3.34] sorted minimizers[M::main::117.963*3.34] loaded/built the index for 702657 target...

#GFA to #FASTA file conversion. awk '/^S/{print ">"$2"\n"$3}' in.gfa | fold > out.fa

The dupRadar package gives an insight into the duplication problem by graphically relating the gene expression level and the duplication rate present on it. Thus, failed experiments can be easily identified at a glance

> install.packages(c('ddalpha', 'recipes'))    There is a binary version available but the source version is later:         binary  source needs_compilation ddalpha  1.3.1 1.3.1.1     ...

MUMmer4, a substantially improved version of MUMmer that addresses genome size constraints by changing the 32-bit suffix tree data structure at the core of MUMmer to a 48-bit suffix array, and that offers improved speed through parallel processing...

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...

TelomereHunter is a tool for estimating telomere content from human whole-genome sequencing data. It is designed to take BAM files from a tumor and a matching control sample as input. However, it is also possible to run TelomereHunter with one input...

karyoploteR is an R package to create karyoplots, that is, representations of whole genomes with arbitrary data plotted on them. It is inspired by the R base graphics system and does not depend on other graphics packages. The aim of karyoploteR...

Understanding lastz http://www.bx.psu.edu/~rsharris/rsharris_phd_thesis_2007.pdf

zPicture is a dynamic alignment and visualization tool that is based on blastz alignment program utilized by PipMaker. zPicture alignments can be automatically submitted to rVista 2.0 to identify conserved transcription factor binding...