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Nabil-Fareed Alikhan

MicroBinfie Podcast, 01 What bioinformatics software not to write part 1

microbinfie, podcast2 min read

In this episode we identify areas of “Peak-bioinformatics”. There are a lot of existing bioinformatics software out there - more often than not the new tool you want to write already exists or a new tool cannot effectively improve. We discuss this in terms of genome assembly, read mapping and phylogenetics. Question and comments? SHOW NOTES Generally, novel software is not needed if: There are a plethora of existing tools The problem is more or less solved or its been shown to be unsolvable The underlying technology or problem is now obsolete and/or superceded by other methods. Multiple sequence aligners: MAFFT MUSCLE Whole genome aligners: Mauve Mugsy Sibellia Parsnp Assemblers: SPADES Skesa Velvet Abyss Edena Ray Long read assemblies HGAP Training/wiki/HGAP-2.0 Flye Canu Ra Unicycler Read mapping BWA http://bio- Bowtie2 Minimap2 (BWA better for short reads: BBtools BLAST/BLAT: SMALT Snippy Phenix: bioinformatics/PHEnix Variant callers GATK: VIPR: Varscan2 Workflow managers Bespoke example Snakemake. Nextflow Galaxy Bpipe Phylogenetics: Raxml - Raxml-NG IQTREE FastTree BEAST 1&2 RevBayes Metagenomics Taxonomic classification: Megan, Kraken, SIGMA, MIDAS, metaphlan2, mOTUs. Assemblers: MetaSpades, metaflye, MEGAHIT, MetaVelvet, a lot of single isolate assemblers have been tweaked to run on metagenomes. AMR https://food-safety- ABRICATE ARIBA Too many detection tools: ka0Z1drpA_s3FElfMJe0/edit#gid=0 Other mentioned resources Mentioned Recent review. Zhang W, Chen J, Yang Y, Tang Y, Shang J, Shen B (2011) A Practical Comparison of De Novo Genome Assembly Software Tools for Next-Generation Sequencing Technologies. PLoS ONE 6(3): e17915. The Assemblerthon: Blog post describing that BWA better for short reads: the-future-of-bwa The science web: to-have-their-own-personal-short-read-aligner-by-2016/