GitHub - wangqinhu/fgreseq: Resequencing project for Fusarium graminearum

This repository keeps the source codes (master branch) and data (data branch) used for Fusarium graminearum resequencing analysis. The main purpose that we share the codes and data is for reproducibility and transparency.

The final analysis results have been published as follow:

Wang Q, Jiang C, Wang C, Chen C, Xu JR, Liu H. (2017) Characterization of the two-speed subgenomes of Fusarium graminearum reveals the fast-speed subgenome specialized for adaption and infection. Frontiers in Plant Science 8, 140.

See the fulltext in http://journal.frontiersin.org/article/10.3389/fpls.2017.00140/full or download the pdf here.

Name		Name	Last commit message	Last commit date
Latest commit History 79 Commits
Snap		Snap
blast		blast
.gitignore		.gitignore
2speed.R		2speed.R
2speed.supp.R		2speed.supp.R
2speed.supp.sh		2speed.supp.sh
README.md		README.md
bar_ir.R		bar_ir.R
bowtie-build.sh		bowtie-build.sh
bowtie2-build.sh		bowtie2-build.sh
chipseq.sh		chipseq.sh
circos.run.sh		circos.run.sh
circos2.run.sh		circos2.run.sh
circos_spe.run.sh		circos_spe.run.sh
classpro.sh		classpro.sh
combcds.pl		combcds.pl
corr_plot.R		corr_plot.R
coverage.rnaseq.sh		coverage.rnaseq.sh
coverage.sh		coverage.sh
exhg.pl		exhg.pl
ext.svf.sh		ext.svf.sh
extexon.pl		extexon.pl
extfir.pl		extfir.pl
extfir_gtf.pl		extfir_gtf.pl
extgene.interval.pl		extgene.interval.pl
fa2phy.pl		fa2phy.pl
featurecounts.sh		featurecounts.sh
fets.R		fets.R
fir.R		fir.R
fir.sh		fir.sh
fmt_coverage.sh		fmt_coverage.sh
fmtgtf.pl		fmtgtf.pl
fmtseq.pl		fmtseq.pl
gc.interval.sh		gc.interval.sh
gccontent.pl		gccontent.pl
gccontent.sh		gccontent.sh
gene2density.pl		gene2density.pl
gff2circos.pl		gff2circos.pl
gff2circos.sh		gff2circos.sh
gff2fasta.pl		gff2fasta.pl
go_fast.R		go_fast.R
go_ir.R		go_ir.R
hisat-build.sh		hisat-build.sh
hisat.sh		hisat.sh
isc		isc
ivenn.sh		ivenn.sh
len_gc.pl		len_gc.pl
merge-density.sh		merge-density.sh
merge_bam.sh		merge_bam.sh
merge_bam_rnaseq.sh		merge_bam_rnaseq.sh
merge_diff_cpm.sh		merge_diff_cpm.sh
merge_svf.pl		merge_svf.pl
mummer2Vcf.pl		mummer2Vcf.pl
mummer_var.sh		mummer_var.sh
papro.sh		papro.sh
parse_blast.pl		parse_blast.pl
phi.sh		phi.sh
pnps.R		pnps.R
pnps.pl		pnps.pl
pnps.run.sh		pnps.run.sh
rnaseq.2speed.sh		rnaseq.2speed.sh
rnaseq.diff.R		rnaseq.diff.R
rnaseq.display.R		rnaseq.display.R
rnaseq.run.sh		rnaseq.run.sh
secretome2circos.pl		secretome2circos.pl
secretome2circos.sh		secretome2circos.sh
select_homo.pl		select_homo.pl
seq2snp.sh		seq2snp.sh
signalp2circos.pl		signalp2circos.pl
signalp2circos.sh		signalp2circos.sh
smpro.sh		smpro.sh
snpEff-build.sh		snpEff-build.sh
snpEff.config		snpEff.config
snpEff.sh		snpEff.sh
split_gene.run.sh		split_gene.run.sh
svf2seq.pl		svf2seq.pl
svf2spe_vcf.pl		svf2spe_vcf.pl
svf2spe_vcf.sh		svf2spe_vcf.sh
tree.sh		tree.sh
var_freq.R		var_freq.R
var_stats.sh		var_stats.sh
vcf2density.pl		vcf2density.pl
vcf2density.sh		vcf2density.sh
vcf2density_spe.sh		vcf2density_spe.sh
vcf2fasta.pl		vcf2fasta.pl
vcf_filter.sh		vcf_filter.sh
vcfem.R		vcfem.R
venn_ir.R		venn_ir.R
venn_lof.sh		venn_lof.sh
venn_var.sh		venn_var.sh

wangqinhu/fgreseq

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