Illumina based assembly pipeline steps !
Illumina Merge re-sequenced FastQ files (cat) Read QC (FastQC) Adapter...index alignments (SAMtools) Primer sequence removal (iVar; amplicon data...ltiple variant calling and consensus sequence generation routes (iVar varia...ade assignment, mutation calling and sequence...891 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...877 days ago
List of comparative genomics resources !
...me comparisons and functional analysis. MBGD -- Microbial genom...rative analysis of completely sequenced microbial genomes. MEGA...ide functional and structural analysis. PReMod -- a database of...er (ESTs and full-length mRNA sequences organized into clusters that...691 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...b. Sachidandam et al. 2001. A map of human genome sequence variation containing 1.42 mi...le gene. Genet. Res. 23: 23-35. Understanding sequence...691 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...674 days ago
Must read paper and books in evolution biology !
1. *Nick Barton:* - The textbook "Evolution" by Nick Barton, with resources for...b. Sachidandam et al. 2001. A map of human genome sequence variation containing 1.42 mi...le gene. Genet. Res. 23: 23-35. Understanding sequence...591 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...558 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...558 days ago
Interesting Bioinformatics Resources !
1. a reproducible workflow. https://www.youtube.com/watch?v=s3JldKoA0zw This two minute video will change your mind on reproducible research 2. Parallel...555 days ago
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