Illumina based assembly pipeline steps !
...alignments (SAMtools) Primer sequence removal (iVar; amplicon data on...variant calling and consensus sequence generation routes (iVar variants and c...sment report (QUAST) Lineage analysis (Pangolin) Clade assignment, mutation calling and sequence quality checks (Nextclade) Individual variant screens...886 days ago
Useful Bioinformatics Analysis Tools !
CoMeta Classificier of reads from metagenomic sequencing experiment...mpression of protein multiple sequence alignment files, Bioinfo...Sz., Compression of DNA sequences in FASTQ format, Bioinf...ssor of collections of genome sequences. • Deorowic...873 days ago
List of comparative genomics resources !
...enomes A data management and analysis system for metagenomes I...rative analysis of completely sequenced microbial genomes. MEGA...phylogenetic and evolutionary analysis. PhyloPat -- the phyloge...er (ESTs and full-length mRNA sequences organized into clusters that...687 days ago
Online resources on must-read papers in evolutionary biology, for a literature club
1. *Nick Barton:* - The textbook "Evolution" by Nick Barton, with resources for...1b. Sachidandam et al. 2001. A map of human genome sequence variation containing 1.42 mi...ble gene. Genet. Res. 23: 23-35. Understanding sequence...686 days ago
Understanding DUMP files from NCBI Taxonomy database !
*.dmp files are bcp-like dump from GenBank taxonomy database General information. Field terminator is "\t|\t" Row...n subtree root flag (1 or 0) -- 1 if this subtree has no sequence...670 days ago
Must read paper and books in evolution biology !
1. *Nick Barton:* - The textbook "Evolution" by Nick Barton, with resources for...1b. Sachidandam et al. 2001. A map of human genome sequence variation containing 1.42 mi...ble gene. Genet. Res. 23: 23-35. Understanding sequence...587 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/em...554 days ago
Tools for Differential expression analysis
apeglm - https://bioconductor.org/packages/release/bioc/html/apeglm.html ashr - https://github.com/stephens999/ashr, https://cran.r-project.org...554 days ago
Interesting Bioinformatics Resources !
1. a reproducible workflow. https://www.youtube.com/wa...icle/pii/S2666389921002300 4. A Reproducible Data Analysis Workflow with R Markdown, Git...putational workflows is automated using continuous analysis https://www.nature.com/a...550 days ago
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