cotton genome variations database

Software List

Program	Version	URL
bcftools	1.7	http://samtools.github.io/bcftools/bcftools.html
Bismark	0.22.1	https://github.com/FelixKrueger/Bismark
BWA	0.7.15-r1140	https://github.com/lh3/bwa
clusterprofiler	3.14.2	http://www.bioconductor.org/packages/release/bioc/html/clusterProfiler.html
Cutadapt	2.7	https://pypi.org/project/cutadapt/
Deseq2	1.26.0	http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html
GATK	4.0.4.0	https://software.broadinstitute.org/gatk/
Hisat2	2.0.5	http://ccb.jhu.edu/software/hisat2/index.shtml
Interproscan	5.25-64.0	http://www.ebi.ac.uk/interpro/search/sequence-search
ITAK	1.7	https://github.com/kentnf/iTAK
JBrowse	1.16.6	https://jbrowse.org/
LTR_FINDER	1.0.6	https://code.google.com/archive/p/ltr-finder/
LTRharvest	1.5.9	http://genometools.org/pub/
MACS2	2.1.2	https://pypi.org/project/MACS2/
MCScanX	-	http://chibba.pgml.uga.edu/mcscan2/
minimap2	2.16 (r922)	https://github.com/lh3/minimap2/releases
MUMMER	3.0	http://mummer.sourceforge.net/
Primer3	2.4.0	https://github.com/primer3-org/primer3
R-WGCNA	1.68	https://cran.r-project.org/web/packages/WGCNA/index.html
SAMtools	1.7	http://samtools.sourceforge.net/
Sequenceserver	2.0.0	http://sequenceserver.com/
StringTie	1.3.3b	http://ccb.jhu.edu/software/stringtie/
Trimmomatic	0.36	http://www.usadellab.org/cms/?page=trimmomatic
Vcftools	0.1.15	http://vcftools.sourceforge.net/

Method

Gene annotation manual

Variation query manual

Co-expression-G.hirsutum moudle manual