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 “formula” file Note: The default...949 days ago
Illumina based assembly pipeline steps !
Illumina Merge re-sequenced FastQ files...rimer sequence removal (iVar; amplicon data only) Duplicate read marking...ts and consensus; default for amplicon data || BCFTools, BEDTools; defaul...y Primer trimming (Cutadapt; amplicon data only) Choice of multiple ass...892 days ago
Useful Bioinformatics Analysis Tools !
CoMeta Classificier of reads from metagen...ace-saving solution for raw sequencing data, Bioinformatics, 20...k-mer-based compression of sequencing data, Scientific Reports,&nbs...ki, L., Disk-based compression of data from genome sequencing, ...878 days ago
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List of comparative genomics resources !
...coDing Orthologous Regions A database resource of developmental...arative Genometrics (CG) -- a database dedicated to biometric co...MBGD -- Microbial genome database for comparative analysis...hensive suite of programs and databases for comparative analysis...692 days ago
Understanding DUMP files from NCBI Taxonomy database !
*.dmp files are bcp-like dump from GenBank taxonomy database General information. Fi...t node id in GenBank taxonomy database rank -- rank of t...this subtree has no sequence data yet comments -- free-...med_id -- unique id in PubMed database (0 if not in PubMed) med...675 days ago
Interesting Bioinformatics Resources !
1. a reproducible workflow. https://www.youtube.com...false 3. Common-sense approaches to sharing tabular data alongside publication ht...nce/article/pii/S2666389921002300 4. A Reproducible Data Analysis Workflow with R Mark...556 days ago
Common steps for reads mapping !
Mapping reads to a ref...r that is appropriate for your type of data and research question. I...indexing tools. Prepare the read data: The reads should be in a for...ypically involves specifying the input data, reference genome, and output...438 days ago
Calculate the significance of the difference between two trends
To calculate the significance of the difference betwe...hile H1 might be that there is a significant difference. Collect data on the two trends. Make sure that the data is independent, normally dist...433 days ago
Free Books on Machine Learning and Artificial Intelligent !
An Introduction to Statistical LearningT...o wishes to use contemporary tools for data analysis. https://hastie.su....mains/ISLR2/ISLRv2_website.pdf Python Data Science HandbookYou’ll...eaning, manipulating, and transforming data — or building machine l...431 days ago