Basic Structure of Snakemake Pipeline Run !
/user/snakemake-demo$ ls config.json data envs scripts slurm-240702.out Snakefile data = mock data for the snakefile to use Snakefile = name of the snakemake &ldq...962 days ago
Illumina based assembly pipeline steps !
Illumina Merge re-sequenced FastQ files (ca...tie 2) Sort and index alignments (SAMtools) Primer sequence removal (iV...onal) Alignment-level QC (picard, SAMtools) Genome-wide and amplicon co...Intersect variants across callers (BCFTools) De novo assembly Primer...905 days ago
Useful Bioinformatics Analysis Tools !
CoMeta Classificier of reads from metagenomic sequencing experiments. • Kawulok, J., Deorowicz, S., CoMeta: Classification of Metagenomes Using...891 days ago
List of comparative genomics resources !
3D-GENOMICS -- A Database to Compare Structural and Functi...nt model organisms. Phylemon -- A suite of web tools for molecular evolution, phyl...tegrates a selected suite of more than 20 different tools from the most popular stand-a...705 days ago
Tools for Sequence translation !
BOrf - https://github.com/betsig/borf CodAn - https://github.com/pedronachtigall/CodAn EMBOSS-Sixpack - https://www.ebi.ac.uk/Tools/st/emboss_sixpack/ esl-trans...572 days ago
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Tools for Differential expression analysis
apeglm - https://bioconductor.org/packages/release/bioc/html/ap...ps://bioconductor.org/packages/release/bioc/html/RUVSeq.html SARTools - https://github.com/PF2-pasteur-fr/SARTools tximport - https:/...572 days ago
Bioinformatics tools to explore SSRs in genomes !
There are several bioinformatics tools that can be used to explore Simple Sequence Re...just a few examples of the many bioinformatics tools available for exploring SSRs....nd research questions, you may find that other tools are more appropriate for your...453 days ago
Common steps for reads mapping !
Mapping reads to a reference genome is an essential step in many ty...per to quickly find matches to the reads. Most mappers have their own indexing tools. Prepare the read data:...451 days ago
Steps to find palindrome in genomes !
Palindromes are sequences of nucleotides that read the same backwar...the genome sequence directly for palindromic sequences using pattern matching tools, such as regular expressions...451 days ago