https://github.com/stenglein-lab/stenglein_lab_scripts
Tip revision: 8f1e3977dc09c9b7e3c9ef2660ca666412500c75 authored by Mark Stenglein on 19 January 2024, 16:30:54 UTC
script to tabulate observed Illumina index sequences
script to tabulate observed Illumina index sequences
Tip revision: 8f1e397
| File | Mode | Size |
|---|---|---|
| Histogram.pm | -rw-r--r-- | 3.5 KB |
| LICENSE | -rw-r--r-- | 1.1 KB |
| Levenshtein.pm | -rw-r--r-- | 6.1 KB |
| README.md | -rw-r--r-- | 282 bytes |
| acc_to_taxid.pm | -rwxr-xr-x | 2.2 KB |
| analyze_sam_error_mode | -rwxr-xr-x | 1.2 KB |
| analyze_sam_flags | -rwxr-xr-x | 2.0 KB |
| assess_sam_trimming | -rwxr-xr-x | 2.3 KB |
| blast_from_fasta | -rwxr-xr-x | 2.9 KB |
| blastmap | -rwxr-xr-x | 2.7 KB |
| build_indexes | -rwxr-xr-x | 2.0 KB |
| calc_lev_matrix | -rwxr-xr-x | 595 bytes |
| column_histo | -rwxr-xr-x | 1.5 KB |
| column_stats | -rwxr-xr-x | 2.6 KB |
| concat_and_sort_gi_dmp_files | -rwxr-xr-x | 1.0 KB |
| concat_fasta_records | -rwxr-xr-x | 2.4 KB |
| concatenate_multiply_sequenced_datasets | -rwxr-xr-x | 4.2 KB |
| concordance_from_sam | -rwxr-xr-x | 3.8 KB |
| consolidate_blast_output | -rwxr-xr-x | 2.7 KB |
| continuous_coverage_from_sam | -rwxr-xr-x | 3.2 KB |
| count_dinucleotide_freqs | -rwxr-xr-x | 2.3 KB |
| create_acc_taxid_mysql_table | -rwxr-xr-x | 637 bytes |
| create_acc_taxid_mysql_table.sql | -rw-r--r-- | 496 bytes |
| create_gb_fsa | -rwxr-xr-x | 3.4 KB |
| create_gi_taxid_mysql_table | -rwxr-xr-x | 528 bytes |
| create_gi_taxid_mysql_table.sql | -rw-r--r-- | 290 bytes |
| cx | -rwxr-xr-x | 12 bytes |
| distribute_db_by_taxid.pl | -rwxr-xr-x | 4.7 KB |
| distribute_fasta_by_blast_taxid.pl | -rwxr-xr-x | 16.7 KB |
| distribute_fasta_by_gsnap_taxid.pl | -rwxr-xr-x | 16.7 KB |
| download_basespace_data | -rwxr-xr-x | 1.6 KB |
| download_sra_data | -rwxr-xr-x | 2.7 KB |
| estimated_fastx_count | -rwxr-xr-x | 3.1 KB |
| export_consensus | -rwxr-xr-x | 1.5 KB |
| extract_insert_map_from_sam | -rwxr-xr-x | 3.7 KB |
| extract_insert_sizes | -rwxr-xr-x | 3.6 KB |
| extract_random_fasta_subset | -rwxr-xr-x | 9.0 KB |
| extract_random_fastq_subset | -rwxr-xr-x | 1.1 KB |
| extract_random_file_subset | -rwxr-xr-x | 912 bytes |
| extract_run_tallies | -rwxr-xr-x | 970 bytes |
| extract_spade_contigs_coverage_levels | -rwxr-xr-x | 1.3 KB |
| extract_spade_contigs_with_coverage_range | -rwxr-xr-x | 1.7 KB |
| extract_strand_bias_from_sam | -rwxr-xr-x | 2.5 KB |
| fasta_analyze_gc | -rwxr-xr-x | 2.5 KB |
| fasta_analyze_lzw | -rwxr-xr-x | 5.5 KB |
| fasta_count | -rwxr-xr-x | 861 bytes |
| fasta_dust_filter | -rwxr-xr-x | 1.8 KB |
| fasta_from_blast | -rwxr-xr-x | 5.1 KB |
| fasta_from_gsnap | -rwxr-xr-x | 4.7 KB |
| fasta_from_sam | -rwxr-xr-x | 4.6 KB |
| fasta_length_stats | -rwxr-xr-x | 2.4 KB |
| fasta_lengths | -rwxr-xr-x | 599 bytes |
| fasta_n_filter | -rwxr-xr-x | 1.1 KB |
| fasta_rna_to_dna | -rwxr-xr-x | 194 bytes |
| fasta_sort_by_size | -rwxr-xr-x | 1.5 KB |
| fasta_to_fasta | -rwxr-xr-x | 474 bytes |
| fasta_trim_bases | -rwxr-xr-x | 2.4 KB |
| fastify | -rwxr-xr-x | 1.3 KB |
| fastq_count | -rwxr-xr-x | 863 bytes |
| fastq_length_stats | -rwxr-xr-x | 2.5 KB |
| fastq_to_fasta | -rwxr-xr-x | 543 bytes |
| fastq_trim_bases | -rwxr-xr-x | 1.3 KB |
| fetch_acc_esummary.pm | -rwxr-xr-x | 3.0 KB |
| fetch_genbank_sequences_by_name | -rwxr-xr-x | 4.8 KB |
| fetch_gi_description | -rwxr-xr-x | 3.7 KB |
| fetch_gi_description.pm | -rwxr-xr-x | 2.9 KB |
| fetch_gi_esummary | -rwxr-xr-x | 1.9 KB |
| fetch_gi_esummary.pm | -rwxr-xr-x | 2.9 KB |
| fetch_nr_nt | -rwxr-xr-x | 2.0 KB |
| filter_fasta_by_size | -rwxr-xr-x | 1.5 KB |
| filter_fastq_by_size | -rwxr-xr-x | 1.2 KB |
| filter_sam_by_pct_id | -rwxr-xr-x | 4.1 KB |
| filter_sam_by_score | -rwxr-xr-x | 2.2 KB |
| filter_unmapped_sam | -rwxr-xr-x | 1.2 KB |
| filter_vcf_by_depth | -rwxr-xr-x | 1.1 KB |
| find_executable | -rwxr-xr-x | 241 bytes |
| gc_window_analysis | -rwxr-xr-x | 1.6 KB |
| gff_to_feature_table | -rwxr-xr-x | 3.2 KB |
| gi_to_taxid.pm | -rwxr-xr-x | 1.9 KB |
| gi_to_taxid_filesearch.pm | -rwxr-xr-x | 1.5 KB |
| identify_last_modified_file | -rwxr-xr-x | 198 bytes |
| identify_pair_linked_contigs | -rwxr-xr-x | 6.1 KB |
| identify_sequences_with_non_canonical_bases | -rwxr-xr-x | 1010 bytes |
| interleave_files | -rwxr-xr-x | 471 bytes |
| intersect_fasta_files | -rwxr-xr-x | 1.0 KB |
| lzw.pm | -rw-r--r-- | 2.2 KB |
| make_matrix | -rwxr-xr-x | 2.8 KB |
| make_sliding_fasta_tiles | -rwxr-xr-x | 2.3 KB |
| make_taxa_matrix | -rwxr-xr-x | 3.7 KB |
| make_tree_tally_matrix | -rwxr-xr-x | 4.5 KB |
| merge_fasta_files | -rwxr-xr-x | 3.2 KB |
| merge_fastq_files | -rwxr-xr-x | 2.1 KB |
| modify_fasta_name | -rwxr-xr-x | 1.1 KB |
| monitor_raid_status | -rwxr-xr-x | 760 bytes |
| pairwise_lev_dist | -rwxr-xr-x | 2.9 KB |
| pretty_tab | -rwxr-xr-x | 1.3 KB |
| print_ns | -rwxr-xr-x | 95 bytes |
| pubmed_xml_to_authors | -rwxr-xr-x | 3.2 KB |
| qbn | -rwxr-xr-x | 11.9 KB |
| qbp | -rwxr-xr-x | 10.7 KB |
| qbx | -rwxr-xr-x | 11.0 KB |
| quantify_soft_trimming_from_sam | -rwxr-xr-x | 3.8 KB |
| rc | -rwxr-xr-x | 1.1 KB |
| reconcile_fastq_to_fasta | -rwxr-xr-x | 2.2 KB |
| reconcile_genbank_to_fasta | -rwxr-xr-x | 1.6 KB |
| reconcile_read2_file | -rwxr-xr-x | 4.7 KB |
| remove_empty_files | -rwxr-xr-x | 49 bytes |
| replace_fasta_header_with_organism | -rwxr-xr-x | 1.1 KB |
| replace_fasta_header_with_organism_via_fetch | -rwxr-xr-x | 5.6 KB |
| run_once_file_exists | -rwxr-xr-x | 1017 bytes |
| run_tbl2asn | -rwxr-xr-x | 570 bytes |
| sam_to_bam | -rwxr-xr-x | 213 bytes |
| self_blastn | -rwxr-xr-x | 173 bytes |
| setup_databases.sh | -rwxr-xr-x | 1.8 KB |
| setup_server.sh | -rwxr-xr-x | 28.9 KB |
| shared_fasta_records | -rwxr-xr-x | 2.7 KB |
| simple_scheduler | -rwxr-xr-x | 4.2 KB |
| sort_by_column | -rwxr-xr-x | 1.3 KB |
| spaces_to_tabs | -rwxr-xr-x | 40 bytes |
| split_fasta_file | -rwxr-xr-x | 3.5 KB |
| split_fasta_file.old | -rwxr-xr-x | 2.2 KB |
| split_fasta_file_into_single_sequences | -rwxr-xr-x | 2.4 KB |
| sra_to_fastq | -rwxr-xr-x | 1.2 KB |
| tabulate_mismatches_from_sam | -rwxr-xr-x | 9.5 KB |
| tally_hits_from_sam.pl | -rwxr-xr-x | 26.4 KB |
| tally_hits_gsnap.pl | -rwxr-xr-x | 25.8 KB |
| tally_hits_universal.pl | -rwxr-xr-x | 39.3 KB |
| tally_sam_hits | -rwxr-xr-x | 1.8 KB |
| tally_sam_scores | -rwxr-xr-x | 217 bytes |
| tally_sam_subjects | -rwxr-xr-x | 591 bytes |
| taxid_descendents | -rwxr-xr-x | 3.0 KB |
| taxid_to_description.pm | -rwxr-xr-x | 1.9 KB |
| taxid_to_kingdom.pm | -rwxr-xr-x | 1.8 KB |
| taxid_to_species_taxid.pm | -rwxr-xr-x | 1.8 KB |
| test_File | -rw-r--r-- | 0 bytes |
| unique | -rwxr-xr-x | 272 bytes |
| unique_fasta_records | -rwxr-xr-x | 2.3 KB |
| what_bc | -rwxr-xr-x | 1.7 KB |
| window_average_verbose | -rwxr-xr-x | 3.9 KB |
