BOL

Example commands to remove lower-case masking: perl -pe '/^[^>]/ and $_=uc' genomic.fna > genomic.unmasked.fna

#Algorithms for computing parsimonious #evolutionary scenarios for genome evolution: https://bmcevolbiol.biomedcentral.com/articles/10.1186/1471-2148-3-2

Overlap Layout Consensus assembly http://www.cs.jhu.edu/~langmea/resources/lecture_notes/assembly_olc.pdf #OLC #Assembly

Comparison of the two major classes of #assembly algorithms: overlap–layout–consensus and de-bruijn-graph https://academic.oup.com/bfg/article/11/1/25/191455

hybrid assembly pipeline for bacterial genomes with Unicycler: https://github.com/rrwick/Unicycler #Unicycler #Hybrid #Bacteria

Sort a file with column 2: sort -g -k 2,2 allPacbio.fa.fai > sorted.fai #sort #file #column

Get the reads in fastq file: awk '{s++}END{print s/4}' file.fastq #reads #count #ngs #fastq

De Bruijn graph Tutorial http://www.cs.jhu.edu/~langmea/resources/lecture_notes/assembly_dbg.pdf #Assembly #Tutorial #DeBruijn

Understanding alignment https://www.cs.umd.edu/class/fall2011/cmsc858s/Alignment.pdf #Alignment #Learn

Genetic algorithms with Python https://github.com/handcraftsman/GeneticAlgorithmsWithPython #Python #GA

We are still working on to fix some of the missing BOL data. sorry for the inconvenience caused. #BOL #Work #Data #Missing #Recover

Sorry, due to server transfer BOL is facing some difficulties loading data ... we will try to resolve it ASAP.

Remove duplicated lines from text file. $ awk '!seen[$0]++' allIds #duplicate #lines #remove #awk

Toy example comparing several MSA algorithms http://wiki.bits.vib.be/index.php/Multiple_sequence_alignment #Alignment #MSA #Algorithms

Scripts for Phylogenetics at https://github.com/gigascience/paper-jarvis2014 #Phylogenetics #Script #Perl