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https://github.com/carden24/Bioinformatics_scripts
21 January 2021, 14:11:56 UTC
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Tip revision: 020af3000eeca9c2e270be798fe7264ece87f22b authored by Erick Cardenas on 30 September 2018, 20:38:24 UTC
Delete create_multiple_f.sh
Tip revision: 020af30
File Mode Size
Barcode_Preparation_Toolbox
dist
.gitignore -rw-r--r-- 58 bytes
GET_LINEAGES_NCBI.EC.py -rw-r--r-- 7.7 KB
GET_LINEAGES_NCBI.py -rwxr-xr-x 7.2 KB
HMM_search_and_parse_and_extract.py -rw-r--r-- 14.3 KB
HMM_search_and_parse_and_extract_2.py -rw-r--r-- 14.7 KB
Nonpareil.R -rwxr-xr-x 7.8 KB
add_coverage_to_fasta_contigs.py -rw-r--r-- 2.6 KB
add_coverage_to_fasta_contigs_2.py -rw-r--r-- 2.6 KB
add_lineage_to_dictionary.py -rw-r--r-- 4.4 KB
add_lineage_to_dictionary_2.py -rw-r--r-- 4.4 KB
all_hmm_ps.len -rw-r--r-- 4.2 KB
all_hmm_ps_2.len -rw-r--r-- 4.2 KB
annotate_blast.py -rw-r--r-- 921 bytes
annotate_blast_part2.py -rw-r--r-- 837 bytes
bam_to_fastq.sh -rwxr-xr-x 292 bytes
bowtie2sam.pl -rw-r--r-- 2.1 KB
calculate_coverage_from_bed_coverage.R -rwxr-xr-x 665 bytes
calculate_sequence_conservation.py -rw-r--r-- 616 bytes
clean_blast_result.py -rwxr-xr-x 308 bytes
compare_lists.py -rw-r--r-- 2.2 KB
concatenate_cazy_results.R -rwxr-xr-x 1.9 KB
convert_fasta_to_list.py -rwxr-xr-x 312 bytes
correct_cazy_dictionary.py -rwxr-xr-x 3.0 KB
count_hmmer_hits.py -rw-r--r-- 316 bytes
create_detailed_bed_graph.R -rwxr-xr-x 1.5 KB
create_foly_dictionary.py -rwxr-xr-x 857 bytes
create_max_bits_dictionary.py -rwxr-xr-x 377 bytes
create_multiple_hmm.sh -rwxr-xr-x 280 bytes
create_newcazy_dictionary.py -rwxr-xr-x 3.3 KB
create_newcazy_dictionary_with_subfamilies.py -rwxr-xr-x 3.4 KB
create_sample_by_OTU_table.R -rwxr-xr-x 1.3 KB
dbCAN_HMM_Genomes.py -rwxr-xr-x 5.0 KB
dereplicate_fasta.py -rw-r--r-- 2.1 KB
estimate_gene_coverage_from_simulated_fasta.py -rw-r--r-- 7.0 KB
estimate_gene_coverage_from_simulated_fasta_v_cryptococcus.py -rw-r--r-- 7.5 KB
estimate_gene_coverage_from_simulated_fasta_v_neurospora.py -rw-r--r-- 7.5 KB
estimate_richness_by_family.R -rwxr-xr-x 1.1 KB
extract_sam_columns.py -rwxr-xr-x 829 bytes
fasta2stockholm.pl -rwxr-xr-x 39.4 KB
fasta_removal.py -rw-r--r-- 1.5 KB
fasta_to_stockholm.py -rwxr-xr-x 263 bytes
fastaselection_nucleotide.py -rwxr-xr-x 1.4 KB
fastaselection_protein.py -rwxr-xr-x 2.5 KB
fastaselection_protein_v2.py -rw-r--r-- 726 bytes
fastq-to-fasta.py -rwxr-xr-x 1.4 KB
fastq_to_fasta.py -rw-r--r-- 2.8 KB
fastqcing.sh -rwxr-xr-x 186 bytes
fetch_genome_xml.py -rwxr-xr-x 640 bytes
filter_blast_by_query_coverage.py -rwxr-xr-x 888 bytes
filter_by_size.py -rwxr-xr-x 2.7 KB
filter_fasta.py -rw-r--r-- 697 bytes
filter_fasta_by_completeness.py -rw-r--r-- 721 bytes
filter_mothur_biome.py -rw-r--r-- 1.0 KB
find_linear_correlation.R -rwxr-xr-x 293 bytes
find_unique_contigs.hit.py -rwxr-xr-x 621 bytes
fq_gz-fa.py -rwxr-xr-x 467 bytes
fq_gz-first_100000.fa.py -rw-r--r-- 461 bytes
gbk2faa.txt -rwxr-xr-x 2.9 KB
gbk2fna.txt -rwxr-xr-x 2.2 KB
genbank_to_fasta.py -rw-r--r-- 2.2 KB
genbank_to_table.py -rwxr-xr-x 2.1 KB
genome_len_dict3.pkl -rwxr-xr-x 47.4 KB
get_full_name.py -rwxr-xr-x 120 bytes
get_gi_number_from_cazy_blast.py -rw-r--r-- 664 bytes
get_gi_number_from_cazy_fasta.py -rw-r--r-- 668 bytes
get_hmm_len.py -rw-r--r-- 754 bytes
get_name_and_description.py -rwxr-xr-x 288 bytes
get_protein_from_nucleotide_accession.py -rw-r--r-- 4.5 KB
get_protein_from_nucleotide_accession_v2.py -rw-r--r-- 4.9 KB
get_protein_with_gi_number.py -rw-r--r-- 923 bytes
heatmap_3.R -rwxr-xr-x 15.4 KB
heatmap_colors_in.cols.R -rwxr-xr-x 692 bytes
hmmscan-parser.sh -rwxr-xr-x 1.5 KB
len_stats_from.fasta.py -rwxr-xr-x 709 bytes
modify_dereplicated.py -rw-r--r-- 1.0 KB
multi_selection.py -rw-r--r-- 2.0 KB
multi_selection_for7.py -rw-r--r-- 5.6 KB
multiline_fasta_to_fasta.py -rw-r--r-- 384 bytes
nmds.R -rwxr-xr-x 2.1 KB
normalize_kegg.py -rwxr-xr-x 3.3 KB
parse_hmm_tabular_output.sh -rwxr-xr-x 280 bytes
parse_taxonomic_distribution_and_activities_from_cazy_htmls.py -rw-r--r-- 3.7 KB
parse_taxonomic_distribution_from_cazy_htmls.py -rw-r--r-- 2.8 KB
parse_taxonomy.py -rw-r--r-- 1.0 KB
parse_xml_result.py -rwxr-xr-x 977 bytes
pheatmap.R -rwxr-xr-x 1.6 KB
pkl_to_csv.py -rw-r--r-- 444 bytes
plot_gene_expression.R -rwxr-xr-x 1.2 KB
print_checkm_output.py -rw-r--r-- 440 bytes
process_Dave_data.sh -rwxr-xr-x 189 bytes
progress_bar.py -rw-r--r-- 892 bytes
progress_bar.pyc -rw-r--r-- 838 bytes
quality-trim.py -rwxr-xr-x 1.3 KB
quality-trim_to_gz.py -rwxr-xr-x 1.2 KB
readme.md -rw-r--r-- 287 bytes
remoteblastp.py -rwxr-xr-x 900 bytes
remoteblastp_vs_refsq.py -rw-r--r-- 901 bytes
rename_fasta-to-fasta.py -rw-r--r-- 393 bytes
retrieve_genbank_annotation.py -rwxr-xr-x 1.5 KB
retrieve_genbank_record.to.fasta.py -rwxr-xr-x 866 bytes
retrieve_genbank_record.to.fasta.v2.py -rwxr-xr-x 1.6 KB
retrieve_lineages.py -rw-r--r-- 1.4 KB
retrieve_taxonomy_from_accession_numbers.py -rw-r--r-- 1.4 KB
retrieve_taxonomy_from_accession_numbers_v2.py -rw-r--r-- 856 bytes
retrieve_taxonomy_from_gis.py -rw-r--r-- 1.8 KB
retrieve_taxonomy_from_gis_V2.py -rw-r--r-- 1.8 KB
score_OTU_from_fasta.py -rwxr-xr-x 805 bytes
score_and_filter.hmm.results.py -rwxr-xr-x 1.1 KB
score_blast.py -rwxr-xr-x 1.5 KB
score_blast2.py -rwxr-xr-x 1.7 KB
score_blast_and_normalize.py -rwxr-xr-x 1.5 KB
score_blast_for_redundancy.py -rw-r--r-- 953 bytes
score_blast_for_redundancy.v2.py -rw-r--r-- 1.0 KB
score_blast_nofilter.py -rwxr-xr-x 1.5 KB
score_blast_results_from_cazy.py -rw-r--r-- 3.5 KB
score_butyrate.py -rw-r--r-- 2.4 KB
score_cogs.py -rw-r--r-- 841 bytes
score_gff.py -rw-r--r-- 1.4 KB
score_keggs.py -rw-r--r-- 2.8 KB
score_nitrogen_blast.py -rwxr-xr-x 1.7 KB
score_paired_ends.py -rwxr-xr-x 3.0 KB
score_taxonomy_from_megan.py -rw-r--r-- 1.2 KB
select.sequences.from.fasta.py -rw-r--r-- 911 bytes
separate_AA_from_cazy.py -rw-r--r-- 753 bytes
separate_bowtie_mapping.R -rwxr-xr-x 561 bytes
sff_to_trimmed.fastq.py -rwxr-xr-x 257 bytes
split_pairs.py -rw-r--r-- 1004 bytes
splitter_vHPC.R -rwxr-xr-x 882 bytes
stats_ on _blast.py -rwxr-xr-x 1.8 KB
stats_assemstats.py -rw-r--r-- 2.8 KB
stats_assemstats2.py -rw-r--r-- 3.0 KB
stats_assemstats3.py -rw-r--r-- 2.4 KB
stats_blast_evalue.py -rwxr-xr-x 584 bytes
stats_contigs.py -rwxr-xr-x 1.9 KB
stats_count_total_bases_from_fasta.py -rwxr-xr-x 378 bytes
stats_count_total_bases_from_fasta_gz.py -rwxr-xr-x 398 bytes
stats_fasta.py -rwxr-xr-x 448 bytes
stats_fasta_fast.py -rw-r--r-- 387 bytes
stats_fasta_fast_2.py -rw-r--r-- 387 bytes
stats_fasta_gz.py -rw-r--r-- 440 bytes
stats_fasta_line.py -rw-r--r-- 254 bytes
stats_fasta_line_2.py -rw-r--r-- 254 bytes
stats_fasta_screed.py -rw-r--r-- 384 bytes
stats_fasta_v2.py -rwxr-xr-x 674 bytes
stats_on_bam.sh -rwxr-xr-x 239 bytes
stats_on_bams.sh -rwxr-xr-x 244 bytes
stats_on_blast_out.py -rwxr-xr-x 1.8 KB
stats_on_fasta_v3.py -rwxr-xr-x 346 bytes
stockholm2fasta.pl -rwxr-xr-x 41.0 KB
stockholm_to_fasta.py -rw-r--r-- 254 bytes
strip_white_space.py -rwxr-xr-x 398 bytes
template_script.python -rwxr-xr-x 171 bytes
three_column_table_to_matrix.R -rwxr-xr-x 793 bytes
translate_file.pl -rwxr-xr-x 13.1 KB
trim_bases_from_fastq.py -rw-r--r-- 1.5 KB
trim_bases_from_fastq_v2.py -rw-r--r-- 3.4 KB
ungap_fasta.py -rw-r--r-- 2.0 KB
ungap_fasta_v2.py -rw-r--r-- 464 bytes
vcfutils.pl -rwxr-xr-x 15.3 KB
vxtractor.pl -rw-r--r-- 21.1 KB

readme.md

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