BOL

SvABA is a method for detecting structural variants in sequencing data using genome-wide local assembly. Under the hood, SvABA uses a custom implementation of SGA (String Graph Assembler) by Jared Simpson, and BWA-MEM by Heng Li....

A computational pipeline for genome-wide detection of putative horizontal gene transfer (HGT) events based on sequence homology search hit distribution statistics Authors: Qiyun Zhu (qiyunzhu@gmail.com), Katharina Dittmar...

ClipCrop for detecting SVs with single-base resolution using soft-clipping information. A soft-clipped sequence is an unmatched fragment in a partially mapped read. To assess the performance of ClipCrop with other SV-detecting tools, we generated...

FASTA and FASTQ are basic and ubiquitous formats for storing nucleotide and protein sequences. Common manipulations of FASTA/Q file include converting, searching, filtering, deduplication, splitting, shuffling, and sampling. Existing tools only...

Osprey is a software platform for the visualization of complex biological interaction networks. Osprey builds data-rich graphical representations from Gene Ontology (GO) annotated interaction data maintained by the BioGRID. Osprey is...

Molinspiration offers broad range of cheminformatics software tools supporting molecule manipulation and processing, including SMILES and SDfile conversion, normalization of molecules, generation of tautomers, molecule fragmentation,...

In this lab we will perform de novo genome assembly of a bacterial genome. You will be guided through the genome assembly starting with data quality control, through to building contigs and analysis of the results. At the end of the lab you will...

Genome assembly tutorial https://bioinformaticsdotca.github.io/high-throughput_biology_2017_module6_lab #tutorial #assembly #tools #steps #pipeline

how to polish a genome assembly https://nanopolish.readthedocs.io/en/latest/quickstart_consensus.html #polish #nanopolish #ont #nanopore #consensus

Using R language with Anaconda https://docs.anaconda.com/anaconda/user-guide/tasks/use-r-language/ #R #Anaconda #Language

Create user with bash $su - joker #user #bash #create

Read a file in terminal $ less file2 #bash #less

Write in a file in bash $ cat >> file then ctrl+d to exit #bash #cat #write

List all the bash command related to time $ apropos time #bash #time #list

Find the file $ locate xgenome or locate fstab #bash #locate

To know about the file detail $ file .face #file #detail

ls -a to list all files #bash #list #ls

To move between current directories $ popd and pushd #pushd #popd #bash

SLURM how to tutorial at #slurm" rel="nofollow">https://www.genouest.org/howto/#slurm #slurm #how #FAQ

Placentals: http://blogs.discovermagazine.com/loom/2012/02/14/mammals-made-by-viruses/ Tunicates: https://www.pnas.org/content/pnas/101/4/986.full.pdf https://www.pnas.org/content/pnas/102/42/15134.full.pdf