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