BOL

I think, you can fix it by running sudo update-alternatives --remove-all python [] sudo apt install python2.7 sudo ln -sf /usr/bin/python2.7 /usr/bin/python [] python -V [] Python 2.7.12

I just came across this paper on arxiv "Estimation of genomic characteristics by analyzing k-mer frequency in de novo genome projects" https://arxiv.org/abs/1308.2012 It is available at ftp://ftp.genomics.org.cn/pub/gce/

Neelam[Val] python []Python 3.5.2 (default, Nov 23 2017, 16:37:01) [GCC 5.4.0 20160609] on linuxType "help", "copyright", "credits" or "license" for more information.>>> q()Traceback (most recent call last): File "", line 1, in NameError:...

You can try many software, but the quickest one are BBTools/kmercountexact.sh To uses approximate counts: khist.sh in=reads.fq khist=khist.txt peaks=peaks.txt To uses exact counts (and thus potentially more memory) kmercountexact.sh...

Alignment algorithms http://vlab.amrita.edu/?sub=3&brch=274&sim=1431&cnt=1 #Alignments #Algo #Blast

I am working on a new genome, and wondering about prediction methods for heterozygosity in the genome. Any tools suggestions and helps are welcome. 

Regioner is an R package for the management and comparison of genomic regions. It offers a set of function for basic manipulation of region sets extending the functionality of GenomicRanges and a powerful and customizable permutation test framework....

Bioinformatics Laboratories https://www.crick.ac.uk/research/labs?topic=19 #Lab #Bioinfo

Bioinformatics analysis could be published in The Nucleus https://link.springer.com/journal/13237

Genobuntu is a software package containing more than 70 software and packages oriented towards NGS. In its current version, Genobuntu supports pre assembly tools, genome assemblers as well as post assembly tools. Commonly used biological...

BLAST stands for Basic Local Alignment Search Tool and was developed by Altschul et al. (1990) and significantly improved by Altschul et al. (1997). It is a very fast search algorithm that is used to separately search protein or DNA...

Align Synteny - Beginning from completed or draft genomes, find shared syntenic regions and align them quickly while accounting for inversions, rearrangements, and duplications. http://www2.decipher.codes/AlignSynteny.html

DECIPHER is a software toolset that can be used for deciphering and managing biological sequences efficiently using the R programming language. The R package is distributed as platform independent source code under the GPL...

RMBlast is a RepeatMasker compatible version of the standard NCBI blastn program. The primary difference between this distribution and the NCBI distribution is the addition of a new program "rmblastn" for use with RepeatMasker and...

GWASpro supports building complex design matrices, by which complex experimental designs that may include replications, treatments, locations and times, can be accounted for in the linear mixed model (LMM). GWASpro is optimized to handle GWAS data...