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Stenglein Lab Scripts
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Mark Stenglein
Mark Stenglein more nt/nr files
Latest commit f0bdcc6 Apr 2, 2019
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Histogram.pm
LICENSE Initial commit Jun 3, 2016
Levenshtein.pm added a bunch Nov 12, 2016
README.md readme Nov 12, 2016
acc_to_taxid.pm switch to using accessions from GIs Aug 2, 2017
analyze_sam_error_mode added a bunch Nov 12, 2016
analyze_sam_flags added a bunch Nov 12, 2016
assess_sam_trimming added a bunch Nov 12, 2016
blast_from_fasta added a bunch Nov 12, 2016
blastmap added a bunch Nov 12, 2016
build_indexes updates Jan 19, 2019
calc_lev_matrix added a bunch Nov 12, 2016
column_histo added a bunch Nov 12, 2016
column_stats added a bunch Nov 12, 2016
concat_and_sort_gi_dmp_files added files for fetching NCBI taxonomy and nr/nt databases Nov 12, 2016
concat_fasta_records added a bunch Nov 12, 2016
concordance_from_sam
consolidate_blast_output added a bunch Nov 12, 2016
continuous_coverage_from_sam added a bunch Nov 12, 2016
count_dinucleotide_freqs added a bunch Nov 12, 2016
create_acc_taxid_mysql_table populate mysql table with accession->taxid mapping info Nov 18, 2017
create_acc_taxid_mysql_table.sql populate mysql table with accession->taxid mapping info Nov 18, 2017
create_gb_fsa seq ids for bunya submission Apr 5, 2018
create_gi_taxid_mysql_table added files for fetching NCBI taxonomy and nr/nt databases Nov 12, 2016
create_gi_taxid_mysql_table.sql load data local Jul 28, 2017
cx more scripts May 24, 2017
distribute_db_by_taxid.pl added a bunch Nov 12, 2016
distribute_fasta_by_blast_taxid.pl switch to using accessions from GIs Aug 2, 2017
distribute_fasta_by_gsnap_taxid.pl added a bunch Nov 12, 2016
download_basespace_data added a bunch Nov 12, 2016
download_sra_data
estimated_fastx_count
export_consensus added a bunch Nov 12, 2016
extract_insert_map_from_sam added a bunch Nov 12, 2016
extract_insert_sizes added a bunch Nov 12, 2016
extract_random_fasta_subset updates Jan 8, 2019
extract_random_fastq_subset added a bunch Nov 12, 2016
extract_random_file_subset
extract_spade_contigs_coverage_levels added a bunch Nov 12, 2016
extract_spade_contigs_with_coverage_range added a bunch Nov 12, 2016
fasta_analyze_gc added a bunch Nov 12, 2016
fasta_analyze_lzw added a bunch Nov 12, 2016
fasta_count added a bunch Nov 12, 2016
fasta_dust_filter added a bunch Nov 12, 2016
fasta_from_blast added a bunch Nov 12, 2016
fasta_from_gsnap added a bunch Nov 12, 2016
fasta_from_sam added a bunch Nov 12, 2016
fasta_length_stats added a bunch Nov 12, 2016
fasta_lengths added a bunch Nov 12, 2016
fasta_n_filter added a bunch Nov 12, 2016
fasta_rna_to_dna added a bunch Nov 12, 2016
fasta_sort_by_size added a bunch Nov 12, 2016
fasta_to_fasta added a bunch Nov 12, 2016
fasta_trim_bases added a bunch Nov 12, 2016
fastify a script to make fasta files from plaintext seqs Jan 11, 2018
fastq_count added a bunch Nov 12, 2016
fastq_length_stats added a bunch Nov 12, 2016
fastq_to_fasta added a bunch Nov 12, 2016
fastq_trim_bases added a bunch Nov 12, 2016
fetch_NCBI_Taxonomy_db updated to reflect move from GI->accession Nov 17, 2017
fetch_acc_esummary.pm fetch accession esummary May 14, 2018
fetch_genbank_sequences_by_name added a bunch Nov 12, 2016
fetch_gi_description added a bunch Nov 12, 2016
fetch_gi_description.pm add fetch_gi_description.pm Jun 30, 2017
fetch_gi_esummary added a bunch Nov 12, 2016
fetch_gi_esummary.pm fixes Feb 8, 2017
fetch_nr_nt more nt/nr files Apr 2, 2019
filter_fasta_by_size added a bunch Nov 12, 2016
filter_fastq_by_size added a bunch Nov 12, 2016
filter_sam_by_pct_id added a bunch Nov 12, 2016
filter_sam_by_score added a bunch Nov 12, 2016
filter_unmapped_sam added a bunch Nov 12, 2016
filter_vcf_by_depth
find_executable added a bunch Nov 12, 2016
gc_window_analysis some updates and add split_fasta_file_into_single_sequences Jan 23, 2017
gff_to_feature_table files for genbank batch submissions Mar 6, 2018
gi_to_taxid.pm switch to using accessions from GIs Aug 2, 2017
gi_to_taxid_filesearch.pm added a bunch Nov 12, 2016
identify_last_modified_file added a bunch Nov 12, 2016
identify_pair_linked_contigs added a bunch Nov 12, 2016
interleave_files added a bunch Nov 12, 2016
intersect_fasta_files
lzw.pm added a bunch Nov 12, 2016
make_matrix
make_sliding_fasta_tiles fixes Feb 8, 2017
make_taxa_matrix make_taxa_matrix Nov 17, 2017
make_tree_tally_matrix
merge_fasta_files added a bunch Nov 12, 2016
merge_fastq_files
modify_fasta_name added a bunch Nov 12, 2016
monitor_raid_status added a bunch Nov 12, 2016
pairwise_lev_dist script to calculate and report pairwise edit distances Nov 17, 2017
pretty_tab added a bunch Nov 12, 2016
print_ns added a bunch Nov 12, 2016
pubmed_xml_to_authors extracts an authors list from Pubmed XML format Nov 17, 2017
qbn
qbp more scripts May 24, 2017
qbx more scripts May 24, 2017
quantify_soft_trimming_from_sam
rc added a bunch Nov 12, 2016
reconcile_fastq_to_fasta added a bunch Nov 12, 2016
reconcile_genbank_to_fasta
reconcile_read2_file added a bunch Nov 12, 2016
remove_empty_files added a bunch Nov 12, 2016
replace_fasta_header_with_organism_via_fetch rewrite fasta headers with organism name first Nov 17, 2017
run_once_file_exists added a bunch Nov 12, 2016
run_tbl2asn files for genbank batch submissions Mar 6, 2018
sam_to_bam added a bunch Nov 12, 2016
self_blastn added a bunch Nov 12, 2016
setup_databases.sh
setup_server.sh more nt/nr files Apr 2, 2019
shared_fasta_records added a bunch Nov 12, 2016
simple_scheduler fixed usage typo Sep 30, 2016
sort_by_column added a bunch Nov 12, 2016
spaces_to_tabs
split_fasta_file added a bunch Nov 12, 2016
split_fasta_file.old added a bunch Nov 12, 2016
split_fasta_file_into_single_sequences some updates and add split_fasta_file_into_single_sequences Jan 23, 2017
sra_to_fastq added a bunch Nov 12, 2016
tally_hits_from_sam.pl added a bunch Nov 12, 2016
tally_hits_gsnap.pl
tally_hits_universal.pl retabbed Jan 22, 2018
tally_sam_hits added a bunch Nov 12, 2016
tally_sam_scores added a bunch Nov 12, 2016
tally_sam_subjects added a bunch Nov 12, 2016
taxid_descendents added a bunch Nov 12, 2016
taxid_to_description.pm added a bunch Nov 12, 2016
taxid_to_kingdom.pm added a bunch Nov 12, 2016
taxid_to_species_taxid.pm added a bunch Nov 12, 2016
unique added a bunch Nov 12, 2016
unique_fasta_records added a bunch Nov 12, 2016
what_bc added a bunch Nov 12, 2016
window_average_verbose added a bunch Nov 12, 2016

README.md

Stenglein Lab scripts

This repository contains scripts created in the Stenglein Lab.

We are working to better document these scripts.

We hope that others find them useful. They are provided "as is". Feedback is welcome at: stengleinlab at gmail

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