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Steps to find all the repeats in the genome !
Last updated 481 days ago by NeelTo find repeats in a genome from 2 to 9 length using a Perl script, you can use the RepeatMasker tool with the "--length" option[0]. Here's a step-by-step guide: Install RepeatMasker: First, you need to install RepeatMasker on your system. You...-
Awesome perl frameworks, libraries and software - PART 4
Last updated 2727 days ago by Neeltjstein/php5-fpm-munin-plugins - A set of Munin plugins for PHP5-FPM perusio/nginx-munin - A set of plugins for monitoring nginx with Munin openresty/lua-resty-memcached - Lua memcached client driver for the ngx_lua based on the... “One code to find them all”: a perl tool to conveniently parse RepeatMasker output files
By Poonam Mahapatra 2395 days agodoua.prabi.fr - One code to find them all is a set of perl scripts to extract useful information from RepeatMasker about transposable elements, retrieve their sequences and get some quantitative information. Assemble RepeatMasker hits into complete TE copies,...Next Generation Sequencing (NGS) Tutorials
By Jitendra Narayan 4140 days ago Comments (31)chagall.med.cornell.edu - Institute of computational biomedicine, Cornell University provide an NGS workshop tutorial at http://chagall.med.cornell.edu/NGScourse/ You can also add your favourite NGS educational material, or workshop tutorial by commenting on this...BUSCO
By Jitendra Narayan 3242 days agohttp://busco.ezlab.org/ - Assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs More at http://busco.ezlab.org/TEannot
By Jit 3049 days agourgi.versailles.inra.fr - We advise to run first the TEdenovo pipeline but it is not compulsory. We suppose you begin by running the TEannot pipeline on the example provided in the directory "db/" rather than directly on your own genomic sequences. Thus, from now on, the...TULIP - The Uncorrected Long read Itegration Pipeline
By Jit 2587 days agogithub.com - #Running TULIP (The Uncorrected Long-read Integration Process), version 0.4 late 2016 (European eel) TULIP currently consists of to Perl scripts, tulipseed.perl and tulipbulb.perl. These are very much intended as prototypes, and additional...Purge Haplotigs: Pipeline to help with curating heterozygous diploid genome assemblies
By Rahul Nayak 2199 days agobitbucket.org - Some parts of a genome may have a very high degree of heterozygosity. This causes contigs for both haplotypes of that part of the genome to be assembled as separate primary contigs, rather than as a contig and an associated haplotig. This can be an...Environmental Genomics Group SciLifeLab/KTH Stockholm
By BioStar 754 days agohttps://github.com/envgen - Useful Metagenomics resources
