Name		Name	Last commit message	Last commit date
Latest commit History 582 Commits
16S		16S
lab_scripts		lab_scripts
mg		mg
tutorials		tutorials
.gitignore		.gitignore
FASTA_deleter_byname.py		FASTA_deleter_byname.py
FASTA_size_and_number.py		FASTA_size_and_number.py
LICENSE.md		LICENSE.md
MSU-16S-arch-usearch8-wrapper.py		MSU-16S-arch-usearch8-wrapper.py
MSU-16S-usearch8-wrapper.py		MSU-16S-usearch8-wrapper.py
PathwayBarplot.R		PathwayBarplot.R
PhyloSeq-Barplot.R		PhyloSeq-Barplot.R
README.md		README.md
amr2b6.py		amr2b6.py
anvi_converter.py		anvi_converter.py
anvi_converter2.py		anvi_converter2.py
assembly_script_builder.py		assembly_script_builder.py
bin-coverages.py		bin-coverages.py
bioinformatic_tools.py		bioinformatic_tools.py
bioinformatic_tools.pyc		bioinformatic_tools.pyc
blast_e5_write_subjs_aa.py		blast_e5_write_subjs_aa.py
blast_e5_write_subjs_nt.py		blast_e5_write_subjs_nt.py
combine_assembly.py		combine_assembly.py
combine_matrix_pqvalues.py		combine_matrix_pqvalues.py
combine_stats.py		combine_stats.py
compare-features.py		compare-features.py
compare-gffs.py		compare-gffs.py
compute_gene_abundance.py		compute_gene_abundance.py
compute_usage.py		compute_usage.py
convert_count_to_shared.py		convert_count_to_shared.py
convert_query_format.py		convert_query_format.py
count-mapped-fragments.py		count-mapped-fragments.py
count_cat_tax.py		count_cat_tax.py
count_cat_tax_csv.py		count_cat_tax_csv.py
count_features.py		count_features.py
create_prokka_db.py		create_prokka_db.py
create_sub_fasta.py		create_sub_fasta.py
create_sub_gff3.py		create_sub_gff3.py
csv2tab		csv2tab
dbID_converter.py		dbID_converter.py
depair.py		depair.py
derive_pathway_steps.py		derive_pathway_steps.py
dna2pep.py		dna2pep.py
edit-esom-class-file.py		edit-esom-class-file.py
esom_tracer.py		esom_tracer.py
esom_tracer2.py		esom_tracer2.py
esom_tracer3.py		esom_tracer3.py
esom_tracer4.py		esom_tracer4.py
extract_read_count.py		extract_read_count.py
fast5_1d_to_fastq.py		fast5_1d_to_fastq.py
fasta-get-faa.py		fasta-get-faa.py
fasta-get.py		fasta-get.py
fasta-length-GC.py		fasta-length-GC.py
fasta-list-headers.py		fasta-list-headers.py
fasta-summary.py		fasta-summary.py
fasta_remove_gaps.py		fasta_remove_gaps.py
fastq-summary.py		fastq-summary.py
filter-pathways-table.py		filter-pathways-table.py
filter-table.py		filter-table.py
filter_count_table_by_otu.py		filter_count_table_by_otu.py
filter_count_table_per_sample.py		filter_count_table_per_sample.py
filter_taxonomy.py		filter_taxonomy.py
find-max-column.py		find-max-column.py
format-for-cytoscape.py		format-for-cytoscape.py
genbank_to_faa.py		genbank_to_faa.py
generate_ids.py		generate_ids.py
genes2contigs.py		genes2contigs.py
get-gff.py		get-gff.py
get-long-branches.py		get-long-branches.py
get-sub-prokka-gff.py		get-sub-prokka-gff.py
get-sub-prokka.py		get-sub-prokka.py
get_sub_fasta.py		get_sub_fasta.py
getgffBin.py		getgffBin.py
gff-summary.py		gff-summary.py
gff-to-fasta-search.py		gff-to-fasta-search.py
gff3_searcher.py		gff3_searcher.py
graphs2table.py		graphs2table.py
group_from_filenames.py		group_from_filenames.py
heatmap.py		heatmap.py
homolog_screen.py		homolog_screen.py
keep_count_table_by_otu.py		keep_count_table_by_otu.py
krona_from_humann2.py		krona_from_humann2.py
list_seqs_in_count_tables.py		list_seqs_in_count_tables.py
m5nr_uniprot.py		m5nr_uniprot.py
make-node-attributes.py		make-node-attributes.py
map2list.py		map2list.py
merge_assembled_partitions.pl		merge_assembled_partitions.pl
mod_translate.py		mod_translate.py
modify_tax_summary.py		modify_tax_summary.py
ncbi_genetic_codes.py		ncbi_genetic_codes.py
normalize-coverages.py		normalize-coverages.py
otutaxonomy2tsv.py		otutaxonomy2tsv.py
parse-Qvalues.py		parse-Qvalues.py
parse-pvalues.py		parse-pvalues.py
parse_ale.py		parse_ale.py
parse_bt2.py		parse_bt2.py
parse_sourmash.py		parse_sourmash.py
pathway_table.py		pathway_table.py
pathways2contigs.py		pathways2contigs.py
phylip_ok_v7.py		phylip_ok_v7.py

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lab_scripts

scripts used in the lab's various bioinformatics workflows

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Brazelton-Lab/lab_scripts

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