GitHub - songweizhi/SoftwareCommands: Example commands of some bioinformatic software

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Name		Name	Last commit message	Last commit date
Latest commit History 15 Commits
Autometa		Autometa
GTDB_BLCA		GTDB_BLCA
Gapseq_tutorial_SZ		Gapseq_tutorial_SZ
GenomeTreeTk_demo_data		GenomeTreeTk_demo_data
Katana_cmds.wiki		Katana_cmds.wiki
MarkerMAG_Conda		MarkerMAG_Conda
PacBio_cmds		PacBio_cmds
PhyloBiAssoc		PhyloBiAssoc
.DS_Store		.DS_Store
.gitignore		.gitignore
0_Conda.sh		0_Conda.sh
0_Git_and_GitHub.sh		0_Git_and_GitHub.sh
0_HKUST_HPC3.sh		0_HKUST_HPC3.sh
0_MAC.sh		0_MAC.sh
0_MetaCHIP2.sh		0_MetaCHIP2.sh
0_Perl.sh		0_Perl.sh
0_R.sh		0_R.sh
0_pythonenv.sh		0_pythonenv.sh
ALE.sh		ALE.sh
Abricate.sh		Abricate.sh
AnGST.sh		AnGST.sh
Autometa.sh		Autometa.sh
BBAYs.sh		BBAYs.sh
BLCA_GTDB.sh		BLCA_GTDB.sh
BLCA_SILVA.sh		BLCA_SILVA.sh
BWA.sh		BWA.sh
Barrnap_2020-10-31.sh		Barrnap_2020-10-31.sh
Bbmap.sh		Bbmap.sh
Binning.sh		Binning.sh
Binning_MetaBAT_and_MyCC_CONCOCT.sh		Binning_MetaBAT_and_MyCC_CONCOCT.sh
Binning_refiner.sh		Binning_refiner.sh
Bowtie.sh		Bowtie.sh
Bprom.sh		Bprom.sh
Breseq.sh		Breseq.sh
Busco.sh		Busco.sh
CD-HIT.sh		CD-HIT.sh
COG_annotation.sh		COG_annotation.sh
CONCOCT.sh		CONCOCT.sh
CheckM.sh		CheckM.sh
CheckM2_2022-08-26.sh		CheckM2_2022-08-26.sh
Circlator.sh		Circlator.sh
Clever-toolkit.sh		Clever-toolkit.sh
Clustalw.sh		Clustalw.sh
CompareM_2020-08-31.sh		CompareM_2020-08-31.sh
Conda_CUHK.sh		Conda_CUHK.sh
CoverM.sh		CoverM.sh
DAS_tool.sh		DAS_tool.sh
D_dRep.sh		D_dRep.sh
D_dbCAN.sh		D_dbCAN.sh
D_dbCAN2.sh		D_dbCAN2.sh
Daisy.sh		Daisy.sh
Daisy2_DaisySuite.sh		Daisy2_DaisySuite.sh
Daisy2_DaisySuite_Conda.sh		Daisy2_DaisySuite_Conda.sh
Datasets.sh		Datasets.sh
DeepTools.sh		DeepTools.sh
Diamond.sh		Diamond.sh
Download genomes from NCBI in batch.pptx		Download genomes from NCBI in batch.pptx
E-utilities.sh		E-utilities.sh
ETE3.sh		ETE3.sh
Emirge_2020-10-21.sh		Emirge_2020-10-21.sh
EnrichM.sh		EnrichM.sh
Ezaai.sh		Ezaai.sh
FASTQSim.sh		FASTQSim.sh
FastAAI.sh		FastAAI.sh
FastANI.sh		FastANI.sh
FastTree.sh		FastTree.sh
FigTree.sh		FigTree.sh
Fix_assembly_errors.sh		Fix_assembly_errors.sh
Flye.sh		Flye.sh
GCbias.sh		GCbias.sh
GRiD.sh		GRiD.sh
GTDB-Tk.sh		GTDB-Tk.sh
GTDB-Tk_2020-10-29_r202.sh		GTDB-Tk_2020-10-29_r202.sh
GTDB-Tk_2022-04-11_r207_v2.1.1_CUHK.sh		GTDB-Tk_2022-04-11_r207_v2.1.1_CUHK.sh
Gadi.sh		Gadi.sh
GapSeq.sh		GapSeq.sh
Gblocks.sh		Gblocks.sh
GemErr.sh		GemErr.sh
GemSIM.sh		GemSIM.sh
GenomeTreeTk.sh		GenomeTreeTk.sh
Get_homologues.sh		Get_homologues.sh
Get_taxon.sh		Get_taxon.sh
Gfatools.sh		Gfatools.sh
Ghostx.sh		Ghostx.sh
GraphMB.sh		GraphMB.sh
Growthpred.sh		Growthpred.sh
Guppy.sh		Guppy.sh
HGTree.sh		HGTree.sh
HMMER.sh		HMMER.sh
HgtSIM.sh		HgtSIM.sh
HgtSIM_assessment.sh		HgtSIM_assessment.sh
IQ-Tree.sh		IQ-Tree.sh
I_iRep.sh		I_iRep.sh
InSilicoSeq.sh		InSilicoSeq.sh
Inspector.sh		Inspector.sh
Interproscan.sh		Interproscan.sh
KEGG.sh		KEGG.sh
Kaiju.sh		Kaiju.sh
Katana scratch space from Richard Edwards.sh		Katana scratch space from Richard Edwards.sh
Link_16S_MAG.sh		Link_16S_MAG.sh

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Dr Weizhi Song (songwz03@gmail.com)
Department of Ocean Science (OCES), The Hong Kong University of Science and Technology (HKUST), Hong Kong

songweizhi/SoftwareCommands

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