Table 8 Software for transcriptome analysis.

fastx_toolkit

V0.0.14

http://hannonlab.cshl.edu/fastx_toolkit/

fastp

V0.19.5

https://github.com/OpenGene/fastp

TGICL

V 2.1

https://sourceforge.net/projects/tgicl/files/latest/download

Trinity

V2.8.5

https://github.com/trinityrnaseq/trinityrnaseq

SPAdes

V3.13.1

https://github.com/ablab/spades

BUSCO

V3.0.2

https://busco.ezlab.org/

cd-hit

V4.5.7

https://github.com/weizhongli/cdhit

hisat2

V2.1.0

http://ccb.jhu.edu/software/hisat2/index.shtml

samtools

V1.9

https://github.com/samtools/samtools.git

transrate

V1.0.3

http://hibberdlab.com/transrate/index.html

RSEM

V1.3.1

http://deweylab.biostat.wisc.edu/rsem/

kallisto

V0.46.0

https://pachterlab.github.io/kallisto/download

Salmon

V0.14.1

https://github.com/COMBINE-lab/salmon

bowtie2

V2.3.5.1

https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.3.5.1/

DESeq. 2

V1.24.0

http://bioconductor.org/packages/stats/bioc/DESeq. 2/

edgeR

V3.24.3

http://bioconductor.org/packages/stats/bioc/edgeR/

DEGSeq

V1.38.0

http://bioconductor.org/packages/stats/bioc/DEGSeq/

misa

v2.3.6

http://pgrc.ipk-gatersleben.de/misa/misa.html

TransDecoder

V5.5.0

http://transdecoder.github.io/

HMMER

V3.2.1

http://www.hmmer.org/download.html

bwa

V0.7.9a

https://sourceforge.net/projects/bio-bwa/files/

bcftools

V1.9

https://github.com/samtools/samtools.git

GATK

V3.8

https://software.broadinstitute.org/gatk/download/

BLAST+

V2.9.0

ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.9.0/

Diamond

V0.9.24

https://github.com/bbuchfink/diamond

WGCNA

V1.63

https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/

STEM

V1.3.11

http://www.cs.cmu.edu/~jernst/stem/

maSigPro

V1.56.0

http://www.bioconductor.org/packages/release/bioc/html/maSigPro.html

GSEA

V3.0

http://software.broadinstitute.org/gsea/index.jsp

goatools

V 0.6.5

https://github.com/tanghaibao/goatools

MSigDB

V6.2

http://software.broadinstitute.org/gsea/downloads.jsp

STRING

V11.5

https://string-db.org/

AnimalTFDB

V3.0

http://bioinfo.life.hust.edu.cn/AnimalTFDB/

PlantTFDB

V 4.0

http://planttfdb.cbi.pku.edu.cn/

Pfam

V34.0

http://pfam.xfam.org/

KEGG

V2021.09

http://www.genome.jp/kegg/

eggNOG

V2020.06

http://eggnogdb.embl.de/#/app/home

Rfam

V14.6

http://rfam.janelia.org/

Swiss-Prot

V2021.06

https://www.expasy.org/resources/uniprotkb-swiss-prot

GO

V2021.0918

http://www.geneontology.org/

NR

V2021.10

https://www.ncbi.nlm.nih.gov/public/

PIR idmapping

V2021.06

ftp://ftp.pir.georgetown.edu/databases/idmapping/idmapping.tb.gz