Killifish genomics scripts
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
WGS_seq
annotation
assemble_mt
climate
codonbias
cpp
genome_assembly
longitudinalrnaseq
phylo
pseudogenomes
relax_codeml
trinity
README.md

README.md

killigenomics

Scripts for African killifish genomics. The raw data can be found on NCBI SRA xxxxx. 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