Program versions and specific command line options. 

$1 = prefix for isolate
$2 = path to reference genome in .fasta format

ConDeTri
	perl condetri_v2.2.pl -fastq1=<read1.fastq> -fastq2=<read2.fastq> -prefix=$1 -hq=25 -lq=10 -frac=0.8 -minlen=50 -mh=5 -ml=1 -sc=33
	perl filterPCRdupl_v1.01.pl -fastq1=$1_trim1.fastq -fastq2=$1_trim2.fastq -prefix=$1 -cmp=50

BWA-MEM v0.7.4
# before running, need to index reference genome: bwa index $2
	bwa mem $2 $1_uniq1.fastq $1_uniq2.fastq >$1.sam

Qualimap v2.0.2
	qualimap bamqc -bam $1.bam -outdir <path_to_output_directory>

SAMtools v0.1.19
# before running, need to index reference genome: samtools faidx $2
	samtools view -uS -o $1.bam $1.sam
	samtools sort $1.bam $1
	samtools index $1.bam
	samtools mpileup -P ILLUMINA -C50 -q20 -Q20 -uf $2 $1.bam | bcftools view -cg - > $1.vcf

wgsim (simulating reads from sequences available on GenBank)
	wgsim -N 400000 -1 250 -2 250 <path_to_genome.fasta> <genome.read1.fq> <genome.read2.fq>

MUMmer v3.23
	repeat-match $2 > seq.repeats

SPAdes v3.5.0
	spades.py -k 55 --careful -1 $1_uniq1.fastq -2 $1_uniq2.fastq -o <path_to_outdir>

QUAST v2.3
	python quast.py -R $2 -o <path_to_outdir> <isolate1_contigs.fasta> <isolate2_contigs.fasta> <isolate_n_contigs.fasta>

PAGIT v1.64 (virtual machine downloaded March 3, 2015; iCORN2 downloaded separately)
	ABACAS v1.3.1 
		perl abacas.pl -r $2 -q <$1.fasta> -p nucmer -b -c -t -g $1_gaps -o $1 
	Image
		cat $1.fasta $1.contigsInbin.fas > $1_mappedAndUnmapped.fasta
		perl image.pl -scaffolds $1_mappedAndUnmapped.fasta -prefix $1 -iteration 1 -all_iteration 5 -dir_prefix ite -kmer 55
		perl contigs2scaffolds.pl new.fa new.read.placed 300 500 $1_scaffolds
	iCORN2 v0.95
		perl icorn2.sh $1 180 $1_scaffolds.fa 1 5

LS-BSR v3
Dependencies: Usearch v6.0.307, BLAST v2.2.25, prodigal v2.6.2
	python ls_bsr.py -d <path_to_directory_of_contigs> -u <path_to_usearch> 
	python pan_genome_stats.py –b bsr_matrix_values.txt
	python BSR_to_PANGP.py –b bsr_matrix_values.txt
	python compare_BSR.py -1 <group_of_interest1.txt> -2 <group_of_interest2.txt> –f consensus.fasta –b bsr_matrix_values.txt

PanGP-ubuntu-64bit-1.0.1
	algorithm: Distance Guide 
	sample size: 500
	sample repeat: 10
	amplification coefficient: 10

Gview
	BLAST parameters: filter low complexity sequences; value cut-off 1e-10; alignment length cutoff =100; percent identity cutoff = 80

Parsnp (Harvest v1.0.1)
	parsnp -r $2 -d <path_to_directory_with_contigs> -o <path_to_output_dir> -c

BEDTools
	bedtools maskfasta -fi <input.fa> -bed <bedfile.bed> -fo <outfile_masked.fa>
		where bedfile is tab-delimited textfile: name of chromosome/node	startpos	endpos

BratNextGen- bratPackage downloaded May, 2015
	fixed hyperparameter α = 4 
	recombination estimation algorithm = 20 iterations 
	estimate significance = 100 permutations 
	significance α = 0.05 

Gubbins v1.1.1 virtual machine
	run_gubbins.py <fasta_alignment.aln> 
	gubbins_drawer.py -o <outputname.pdf> -t <alignment_name.final_tree.tre> <alignment_name.recombination_predictions.embl>

PhyloPhlAn
Dependencies: Usearch v5.2.32, FastTree, Muscle v3.8.31
	python phylophlan.py -u <input directory containing .faa files>

fineSTRUCTURE v2.0.4
		perl ./makeuniformrecfile.pl <phasefile.phase> <outputfile.recombfile>
	ChromoPainter-EM
		fs cp -in -i 10 -a 0 0 -j -g <phasefile.phase> -r <path_to_uniform_recombo_file.recombfile> -o <path_to_outputdir_outputprefix>
		perl ./neaverage.pl -o <name of output.txt> <path/to/ChromoPainterEM/Directory/prefix.EMprobs.out>
	ChromoPainter
		fs cp -a 0 0 -n <Ne value> -M <mu value> -g <phasefile.phase> -r <uniform_recombo_file.recombfile> -j -b -o chromoRun
	ChromoCombine
		fs combine -o <output_dir_prefix> -d <chromopainter_output_dir>
		perl ./chromopainterindivrename.pl <idfile.txt> <infileroot> <outputroot>
	fineSTRUCTURE
		fs fs -x 500000 -y 500000 -z 250 <path_to_renamed_chromocombine.chunkcounts.out> <outfile.mcmc.xml>
		fs fs -x 50000 -m T <chromocombine.chunkcounts.out> <fs_outfile.mcmc.xml> <rootname.mcmc.tree.xml>

SplitsTree v4.13.1

PhyML- run using Geneious plugin
	GTR model, gamma distribution, 1000 bootstrap replicates

Path-O-Gen v1.4

MrBayes v3.2.5
	lset nst=6 rates=Invgamma Ploidy =Haploid
	mcmc ngen=10000000 samplefreq =1000 printfreq =1000 

BaTS v0.9 beta
	java -jar BaTS_beta_build2.jar single <inputfile.nex> 100 <number of states>