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Standalone scripts used in the lab's various bioinformatics workflows

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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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Standalone scripts used in the lab's various bioinformatics workflows

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