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killigenomics

Scripts for African killifish genomics. The raw data can be found on NCBI BioProject# PRJNA531796. Data files can be found on Mendeley data https://data.mendeley.com/datasets/f9phgbv4rs/1.

Citation: Relaxed selection limits lifespan by increasing mutation load. R Cui, T Medeiros, D Willemsen, L Iasi, G Collier, M Graef, M Reichard, D R Valenzano (2019) Cell:178.

The main programming language used was PHP >5. They can be most efficiently run with HHVM or PHP 7.

  • genome_assembly/ scripts for performing genome assembly and improvements
  • annotation/ pipelines for genome annotation and improvements
  • trinity/ scripts for performing de novo RNAseq assembly
  • pseudogenomes/ scripts for generating pseudogenomes by switching a SNP based on mapped reads.
  • phylo/ build phylogenetic trees
  • assemble_mt/ contains scripts for mitochondrial genome assembly, annotation and analyses
  • relax_codeml/ contains scripts for alignment generation, gene tree estimation, RELAX and CODEML analyses, amino acid convergence analysis
  • WGS_seq/ contains scripts for processing population resequencing data
  • cpp/ contains c++ code that needs compilation
  • longitudinalrnaseq/ contains scripts to download and reanalyze a previously published longitudinal RNAseq dataset.
  • climate/ PGLS correlations between bioclim, genome size and k
  • codonbias/ compute codon adaptation index and perform simulations

Third-party software packages include:

  • Trimmomatic 0.32
  • Preseq 1.0.2
  • NextClip 1.3.1
  • Discovar de novo 52488
  • NCBI BLAST 2.2.31+
  • BESST (git version 7dba5dd)
  • BESST_RNA (git version 9cc039b)
  • MasurCA 3.2.1
  • Gapfiller 1.10
  • Reapr 1.0.18
  • Redundans 0.13a
  • SGA preQC 0.10.13
  • BWA-MEM 0.7.12-r1039
  • SMALT 0.5.3
  • STAR 2.4.2a
  • BUSCO v2beta4
  • Metassembler 1.3
  • PILON 1.22
  • AllMaps 0.6.9
  • ProgressiveCactus (git version 7af8f26)
  • caper (R package, 1.0.1)
  • RAxML 8.2.4
  • TranslatorX 1.1
  • MAFFT v7.305b
  • Gblocks 0.91b
  • Consel 1.20
  • NOVOPlasty 2.6.3
  • MITOS server (http://mitos.bioinf.uni-leipzig.de/index.py)
  • Trinity 2.1.1
  • Maker 3.0beta
  • Augustus 3.2.1
  • CDHitEST 4.6.4
  • Exonerate 2.2.0
  • RepeatModeler 1.73
  • RepeatMasker 1.331
  • UPhO (git version 4ec1589)
  • MCL 14-137
  • Fasttree 2.1.9
  • HMMER 2
  • GeneWise 2.4.1
  • EvidenceModeler 1.1.1
  • CAFE' 4.0.1
  • TrimAl106 v1.4.rev15
  • CIWOG/GECA (git version ede81942)
  • SGA preQC 0.10.13
  • GATK 3.4.46
  • Samtools/Bcftools 1.2
  • Picard v.1.119
  • APE 5.1
  • PHYTOOLS 0.6.44
  • HyPhy v.2.2.5/v2.3.8
  • PAML 4.8
  • PCOC 07022018
  • Consurf 1.0.6
  • Rate4Site 3.2
  • Package-GFE (05/29/15)
  • scrm 1.7
  • fastStructure 1.0
  • PhyloBayes4.1
  • MSMC 2
  • Bcftools 1.6
  • LDHat (git version 81596e2)
  • Anavar 1.4
  • wgsim 0.3.1-r13
  • featureCounts 1.5.0
  • Deseq 2
  • Angsd 0.918

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Killifish genomics scripts

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