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5 Commits
0_MarkerMAG_Conda
0_MarkerMAG_Conda
 
 
Autometa
Autometa
 
 
GTDB_BLCA
GTDB_BLCA
 
 
Gapseq_tutorial_SZ
Gapseq_tutorial_SZ
 
 
GenomeTreeTk_demo_data
GenomeTreeTk_demo_data
 
 
Katana_cmds.wiki
Katana_cmds.wiki
 
 
PacBio_cmds
PacBio_cmds
 
 
demo_files
demo_files
 
 
images
images
 
 
.gitignore
.gitignore
 
 
0_BioSAK.sh
0_BioSAK.sh
 
 
0_Conda.sh
0_Conda.sh
 
 
0_Gadi.sh
0_Gadi.sh
 
 
0_Katana_R.sh
0_Katana_R.sh
 
 
0_MAC.sh
0_MAC.sh
 
 
0_MarkerMAG.sh
0_MarkerMAG.sh
 
 
0_MetaCHIP.sh
0_MetaCHIP.sh
 
 
0_Perl copy.sh
0_Perl copy.sh
 
 
0_Perl.sh
0_Perl.sh
 
 
0_Raijin.sh
0_Raijin.sh
 
 
0_pythonenv_MAC.sh
0_pythonenv_MAC.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
 
 
CheckM2_2022-08-26.sh
CheckM2_2022-08-26.sh
 
 
CheckM_2020-09-01.sh
CheckM_2020-09-01.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
 
 
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
 
 
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
 
 
FASTQSim.sh
FASTQSim.sh
 
 
FastANI.sh
FastANI.sh
 
 
FastTree.sh
FastTree.sh
 
 
Fix_assembly_errors.sh
Fix_assembly_errors.sh
 
 
Flye.sh
Flye.sh
 
 
GCbias.sh
GCbias.sh
 
 
GTDB-Tk_2020-10-29_r202.sh
GTDB-Tk_2020-10-29_r202.sh
 
 
GTDB-Tk_2022-04-11_r207_v2.1.1.sh
GTDB-Tk_2022-04-11_r207_v2.1.1.sh
 
 
GapSeq.sh
GapSeq.sh
 
 
GapSeq2021.sh
GapSeq2021.sh
 
 
GapSeq2022.sh
GapSeq2022.sh
 
 
GapSeq_js.sh
GapSeq_js.sh
 
 
Gapseq_Gadi.sh
Gapseq_Gadi.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
 
 
Git_and_GitHub.sh
Git_and_GitHub.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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Contact

  • Weizhi Song ([email protected])
  • Center for Marine Science & Innovation (CMSI), University of New South Wales, Sydney, Australia

⚠️ Please note that this repository has been replaced by SoftwareCommands and will no longer receive any updates.

2023-10-25

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some example commands

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