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Name		Name	Last commit message	Last commit date
Rscripts		Rscripts
SOYGO		SOYGO
configFiles		configFiles
get_GitHub_file		get_GitHub_file
.gitignore		.gitignore
00_build_index_hisat2.sh		00_build_index_hisat2.sh
01_lastz_prepare_kmers.sh		01_lastz_prepare_kmers.sh
CopyNumberGen.sh		CopyNumberGen.sh
ExtractSCOs.sh		ExtractSCOs.sh
ExtractSeq.sh		ExtractSeq.sh
Fastq2CA.sh		Fastq2CA.sh
GI2Taxonomy.sh		GI2Taxonomy.sh
GOseq_auto.sh		GOseq_auto.sh
GuessEncoding.sh		GuessEncoding.sh
JRC.sh		JRC.sh
JobBLAST.sh		JobBLAST.sh
JobP128.sh		JobP128.sh
JobQ.sh		JobQ.sh
JobR.sh		JobR.sh
JobR_BLAST.sh		JobR_BLAST.sh
JobR_condo.sh		JobR_condo.sh
JobTime.sh		JobTime.sh
JobTime2.sh		JobTime2.sh
Khmer_interleave.sh		Khmer_interleave.sh
L3.ModuleGen.sh		L3.ModuleGen.sh
LAS-makeSLURMp.py		LAS-makeSLURMp.py
Lines_based_file_deletion.sh		Lines_based_file_deletion.sh
ModuleGen.sh		ModuleGen.sh
N50Calc.pl		N50Calc.pl
PcB_filter_stats.sh		PcB_filter_stats.sh
Quiver_01.sh		Quiver_01.sh
Quiver_02.sh		Quiver_02.sh
README.md		README.md
Rscript_for_plotting_bayescan_results.sh		Rscript_for_plotting_bayescan_results.sh
SAM_to_sortedBAM.sh		SAM_to_sortedBAM.sh
SRAfq2FASTQ.sh		SRAfq2FASTQ.sh
a_loghistory_func.sh		a_loghistory_func.sh
a_longhistory_func.sh		a_longhistory_func.sh
abacas.1.3.1.pl		abacas.1.3.1.pl
acd_func.sh		acd_func.sh
addFastaHeaders.pl		addFastaHeaders.pl
backup		backup
bayes_script.sh		bayes_script.sh
biostar		biostar
biostar.cpp		biostar.cpp
blastXML2Tab.py		blastXML2Tab.py
blast_job_gen.sh		blast_job_gen.sh
blast_wrapper.sh		blast_wrapper.sh
bowtie2_se_noclip.sh		bowtie2_se_noclip.sh
bwa_map_sort.sh		bwa_map_sort.sh
cb		cb
cdgit		cdgit
cegma.sh		cegma.sh
checkBlastStatus.sh		checkBlastStatus.sh
clean_trinity.sh		clean_trinity.sh
combineRawFiles.sh		combineRawFiles.sh
connected_graphs.awk		connected_graphs.awk
count.sh		count.sh
count_fastq.sh		count_fastq.sh
create_sam.sh		create_sam.sh
decison_tree_for_picking_common_strata_for_orthogroups.sh		decison_tree_for_picking_common_strata_for_orthogroups.sh
dos2unix		dos2unix
downloadSRA_ebi.sh		downloadSRA_ebi.sh
edit_sam_files.sh		edit_sam_files.sh
end_time.sh		end_time.sh
extract_seq.sh		extract_seq.sh
extract_seq.sh.save		extract_seq.sh.save
fasta-splitter.pl		fasta-splitter.pl
fasta2fastq.py		fasta2fastq.py
fastaMulti2singleLine.pl		fastaMulti2singleLine.pl
fastaSortByName.pl		fastaSortByName.pl
fasta_distribution.pl		fasta_distribution.pl
fasta_length.py		fasta_length.py
fastarange		fastarange
fastarange.c		fastarange.c
fastasplitn		fastasplitn
fastasplitn.c		fastasplitn.c
fastq-splitter.pl		fastq-splitter.pl
fastq2fasta.sh		fastq2fasta.sh
fastqc_parse.py		fastqc_parse.py
fastqc_stats.sh		fastqc_stats.sh
fasttrans		fasttrans
fasttrans.c		fasttrans.c
filecount		filecount
filter_parllel_log.sh		filter_parllel_log.sh
firstInstanceOf.awk		firstInstanceOf.awk
fna_qual2fastq.py		fna_qual2fastq.py
formatOut2Tab.sh		formatOut2Tab.sh
fq2bam.sh		fq2bam.sh
genome-gaps-as-bed.py		genome-gaps-as-bed.py
get_ip		get_ip
get_taxanomy.sh		get_taxanomy.sh
gff2fasta.pl		gff2fasta.pl
gitgrep		gitgrep
gmap_cdna.sh		gmap_cdna.sh
gsize.sh		gsize.sh
gsnap_pe.sh		gsnap_pe.sh
gsnap_pe2.sh		gsnap_pe2.sh
gsnap_pe_clip.sh		gsnap_pe_clip.sh
gsnap_pe_clip_final.sh		gsnap_pe_clip_final.sh

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common_scripts

my bin directory

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