Frequently used bioinformatics tools for viral genome analysis !
...67 (2012). KMC: Disk-based k-mer counting on a PC. Deorowicz, S., Debudaj-Grabysz, A. & Grabowski, S. BMC Bioinformatics 14, 160 (2013). Kraken: Kraken: ultrafast metagenomic sequen...1090 days ago
Illumina based assembly pipeline steps !
Illumina Merge re-sequenced FastQ files (cat) Read QC (FastQC) Adapter trimming (fastp) Removal of host reads (Kraken 2; optional) Variant calling Read alignment (Bowtie 2) S...920 days ago
Kraken: ultrafast metagenomic sequence classification using exact alignments
Kraken is an ultrafast and highly accurate program for ass...metagenomic data. Using exact alignment of k-mers, Kraken achieves classification accur...to the fastest BLAST program. In its fastest mode, Kraken classifies 100 base pair read...2912 days ago
Metagenomics assembly workshop !!
...sembly Gene Prediction Assembly Evaluation Read Mapping MetaQUAST Binning MaxBin Binning MetaBAT Binning Classification Kraken Taxonomic Sequence Classifica...2617 days ago
Alignment-free sequence comparison tools available for next-generation sequencing data analysis
...ty-reduction technique) Software (C++) https://github.com/marbl/mash Kraken Taxonomic assignment in meta...hensive sequence database Software (C++) https://ccb.jhu.edu/software/kraken/ LMAT Assignment of taxonom...2414 days ago
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Download minikraken database !
...ftp://ftp.ccb.jhu.edu/pub/data/kraken2_dbs/old/minikraken2_v2_8GB_201904.tgz % Total...M (JitMetaENV) ➜ day3 ls minikraken2_v2_8GB_201904.tgz (JitMetaE...tMetaENV) ➜ krakenDB mv ../minikraken2_v2_8GB_201904.tgz . (JitMet...ed.unmapped.R2.fastq.gz > evol1.kraken1257 days ago
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