GitHub - lizhizhong1992/trichy_scripts: scripts written for the trichomonas vaginalis reannotation paper

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scripts written for the trichomonas vaginalis reannotation paper

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Name		Name	Last commit message	Last commit date
Latest commit History 51 Commits
FastFastqFilter.py		FastFastqFilter.py
FastqAssembler.py		FastqAssembler.py
FastqFilter.py		FastqFilter.py
FlatTaxonomyMaker.py		FlatTaxonomyMaker.py
README		README
SlowFastqFilter.py		SlowFastqFilter.py
TaxonomerRunner.py		TaxonomerRunner.py
add_missing_to_basepairs_covered_report.py		add_missing_to_basepairs_covered_report.py
align_Per_SEqID.py		align_Per_SEqID.py
annotate.py		annotate.py
annotate_refseqs.py		annotate_refseqs.py
annotate_refseqs_pool.py		annotate_refseqs_pool.py
assemble_Per_SeqID.new_version.py		assemble_Per_SeqID.new_version.py
assemble_Per_SeqID.py		assemble_Per_SeqID.py
assemble_and_annotate.py		assemble_and_annotate.py
assemble_fastqs.py		assemble_fastqs.py
calc_pi.py		calc_pi.py
fasta_split.pl		fasta_split.pl
filter_classified.py		filter_classified.py
fix_alignments.pl		fix_alignments.pl
gather_est2genome_hits.new_version.py		gather_est2genome_hits.new_version.py
gather_est2genome_hits.py		gather_est2genome_hits.py
gather_refseq.py		gather_refseq.py
get_allele_freqs.py		get_allele_freqs.py
get_gene_nearest_neighbor.py		get_gene_nearest_neighbor.py
get_normalized_counts.py		get_normalized_counts.py
identify_assembly_homology_threshold.py		identify_assembly_homology_threshold.py
identify_common_set.py		identify_common_set.py
identify_common_set_overlaps.py		identify_common_set_overlaps.py
identify_threshold_in_blast_results.py		identify_threshold_in_blast_results.py
make_PWM.py		make_PWM.py
make_config_files_and_run_taxonomer.pl		make_config_files_and_run_taxonomer.pl
make_config_files_and_run_taxonomer.protein.pl		make_config_files_and_run_taxonomer.protein.pl
make_cumulative_cutoff_table.py		make_cumulative_cutoff_table.py
make_database_from_fasta_file.bash		make_database_from_fasta_file.bash
make_database_from_fasta_file.protein.bash		make_database_from_fasta_file.protein.bash
make_flat_taxonomy.py		make_flat_taxonomy.py
percent_basepairs_covered_by_hit.py		percent_basepairs_covered_by_hit.py
pool_annotate.py		pool_annotate.py
quantify_mishits_problem.py		quantify_mishits_problem.py
sort_fastq_file.pl		sort_fastq_file.pl
split_blast_reports_by_sample_and_tier.py		split_blast_reports_by_sample_and_tier.py
summarize_taxonomer_output.py		summarize_taxonomer_output.py
summarize_taxonomer_output_for_R.py		summarize_taxonomer_output_for_R.py
summarize_taxonomer_output_with_coverage.py		summarize_taxonomer_output_with_coverage.py
test.py		test.py
test_Pool.py		test_Pool.py
test_annotate.py		test_annotate.py
tmp.py		tmp.py
wublast_to_substrings.py		wublast_to_substrings.py

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#Daniel Ence
#06/19/2015

#Scripts written for the Trichomonas vaginalis reannotation paper.
#mostly intended for automating the postprocessing of taxonomer outputs.