v2.5

INNUca.py

@@ -10,7 +10,7 @@
 
 Copyright (C) 2016 Miguel Machado <[email protected]>
 
-Last modified: March 23, 2017
+Last modified: April 03, 2017
 
 This program is free software: you can redistribute it and/or modify
 it under the terms of the GNU General Public License as published by
@@ -70,7 +70,7 @@ def get_trueCoverage_config(skipTrueCoverage, trueConfigFile, speciesExpected, s
 
 
 def main():
-	version = '2.4'
+	version = '2.5'
 	args = utils.parseArguments(version)
 
 	general_start_time = time.time()
@@ -201,6 +201,9 @@ def main():
 			print 'Only one fastq file was found: ' + str(fastq_files)
 			print 'Pair-End sequencing is required. Moving to the next sample'
 			continue
+		elif len(fastq_files) == 0:
+			print 'No compressed fastq files were found. Continue to the next sample'
+			continue
 
 		print 'The following files will be used:'
 		print str(fastq_files) + '\n'
@@ -278,7 +281,7 @@ def get_samples(args_inputDirectory, args_fastq, outdir, pairEnd_filesSeparation
 		print ''
 		samples, removeCreatedSamplesDirectories, indir_same_outdir = utils.checkSetInputDirectory(inputDirectory, outdir, pairEnd_filesSeparation_list)
 	elif args_inputDirectory is None:
-		fastq_files = [fastq.name for fastq in args_fastq]
+		fastq_files = [os.path.abspath(fastq.name) for fastq in args_fastq]
 		if fastq_files[0] == fastq_files[1]:
 			sys.exit('Same fastq file provided twice')
 		inputDirectory, samples, removeCreatedSamplesDirectories, indir_same_outdir = get_sample_args_fastq(fastq_files, outdir, pairEnd_filesSeparation_list)

README.md

@@ -219,8 +219,7 @@ Usage
                             Minimum contigs average coverage. After mapping reads
                             back to the contigs, only keep contigs with at least
                             this average coverage (default: 1/3 of the assembly
-                            mean coverage or 10x when mean coverage is lower than
-                            30x)
+                            mean coverage or 10x)
 
     Assembly options:
       --saveExcludedContigs Tells INNUca.py to save excluded contigs (default: False)

modules/assembly_mapping.py

@@ -261,6 +261,8 @@ def save_mapping_statistics(dict_mapping_statistics, outdir):
 	pass_qc = False
 	failing_reason = None
 
+	min_mapping = 0.85
+
 	report_file = os.path.join(outdir, 'assembly_mapping_report.mapping.txt')
 
 	total_reads = 0
@@ -275,11 +277,11 @@ def save_mapping_statistics(dict_mapping_statistics, outdir):
 				total_mapped_reads = dict_mapping_statistics[field]['qc_passed'] + dict_mapping_statistics[field]['qc_failed']
 
 	if total_mapped_reads > 0 and total_reads > 0:
-		if round((float(total_mapped_reads) / float(total_reads)), 2) >= 0.66:
+		if round((float(total_mapped_reads) / float(total_reads)), 2) >= min_mapping:
 			pass_qc = True
 			print 'Mapped reads: ' + str(round((float(total_mapped_reads) / float(total_reads)), 2) * 100) + '%'
 		else:
-			failing_reason = 'Mapped reads: ' + str(round((float(total_mapped_reads) / float(total_reads)), 2) * 100) + '% (lower than 66%)'
+			failing_reason = 'Mapped reads: ' + str(round((float(total_mapped_reads) / float(total_reads)), 2) * 100) + '% (lower than ' + str(min_mapping * 100) + '%)'
 	else:
 		failing_reason = 'No reads were mapped'
 

modules/guess_encoding.py

@@ -40,7 +40,13 @@ def get_encodings_in_range(rmin, rmax):
 	valid_encodings = []
 	for encoding_type, [phred, (emin, emax)] in encoding.items():
 		if rmin >= emin and rmax <= emax:
-			valid_encodings.append([encoding_type, phred])
+			if encoding_type == 'Illumina-1.8':
+				if rmax == emax:
+					valid_encodings.append(['Illumina-1.8', 33])
+				else:
+					valid_encodings.append(['Sanger', 33])
+			else:
+				valid_encodings.append([encoding_type, phred])
 	return valid_encodings if len(valid_encodings) > 0 else None
 
 
@@ -82,7 +88,7 @@ def gather_data_together(data_directory):
 def get_final_encoding(encoding_data):
 	possible_encoding = {}
 	for fastq in encoding_data:
-		if encoding_data[fastq] is not None:
+		if encoding_data[fastq] is not None and encoding_data[fastq]['valid_encodings'] is not None:
 			for i in range(0, len(encoding_data[fastq]['valid_encodings'])):
 				if encoding_data[fastq]['valid_encodings'][i][0] not in possible_encoding:
 					possible_encoding[encoding_data[fastq]['valid_encodings'][i][0]] = 0

modules/mlst.py

@@ -8,7 +8,7 @@
 def getScheme(species):
 	command = ['which', 'mlst']
 	run_successfully, stdout, stderr = utils.runCommandPopenCommunicate(command, False, None, False)
-	mlst_folder = stdout.splitlines()[0]
+	mlst_folder = os.path.abspath(os.path.realpath(stdout.splitlines()[0]))
 	mlst_db_path = os.path.join(os.path.dirname(os.path.dirname(mlst_folder)), 'db', 'species_scheme_map.tab')
 
 	species = species.lower().split(' ')
@@ -55,11 +55,13 @@ def runMlst(contigs, scheme, outdir):
 	if run_successfully:
 		scheme_mlst = stdout.splitlines()[0].split('\t')[1].split('_')[0]
 		st = stdout.splitlines()[0].split('\t')[2]
+		profile = stdout.splitlines()[0].split('\t')[3:]
 
 		report = 'MLST found ST ' + str(st) + ' from scheme ' + scheme_mlst
 		print report
 		with open(os.path.join(outdir, 'mlst_report.txt'), 'wt') as writer:
 			writer.write('#scheme' + '\n' + scheme_mlst + '\n' + '#ST' + '\n' + st + '\n')
+			writer.write('#profile' + '\n' + ' '.join(profile) + '\n')
 			writer.flush()
 
 		if scheme_mlst == scheme:

modules/spades.py

@@ -56,6 +56,8 @@ def define_memory(maxMemory, threads, available_memory_GB):
 	GB_per_thread = 2048 / 1024.0
 
 	minimum_required_memory_GB = GB_per_thread * threads
+	if minimum_required_memory_GB < 4:
+		minimum_required_memory_GB = 4
 
 	if available_memory_GB == 0:
 		print 'WARNING: it was not possible to determine the free available memory!'

modules/trueCoverage_rematch/escherichia_coli.config

@@ -0,0 +1,20 @@
+#reference_file (fasta file full path)
+/home/mpmachado/INNUca/modules/trueCoverage_rematch/escherichia_coli.fasta
+#length_extra_seq (int)
+100
+#maximum_number_absent_genes (int)
+2
+#maximum_number_genes_multiple_alleles (int)
+1
+#minimum_read_coverage (x, int)
+25
+#minimum_depth_presence (x, int)
+5
+#minimum_depth_call (x, int)
+10
+#minimum_depth_frequency_dominant_allele (0-1, double)
+0.60
+#minimum_gene_coverage (0-100, int)
+80
+#minimum_gene_identity (0-100, int)
+70

modules/trueCoverage_rematch/escherichia_coli.fasta

@@ -0,0 +1,34 @@
+>ECs0135
+GGGGGATAATCCGTTGTTACTAAAACGACTTTATATCTTAAGAACGGATTCGCTGGAGACGATGTCGCGGCTGGTGAGTAACCAGCCGCAGGGATAACAATCAAGCAACCTGTACCGGAATCGCTTTCGCGGTACGTTTCATTTCATTGTCGCCTTCAAAATAGGCGACGTTGGGTCGCCAGGTGCGAGCTTCTTCATCTGGCATGGTAACGAAGCTGGCGATGATGACAATATCGCCGACACTGGCGCAGTGGGCCGCCGCACCGTTAACAGAAATAATTCTCGAACCGCGTTCTGCCGCGATGGCATAAGTGGAGAAACGCTTGCCGTTGGTGACATTCCAGATATCAATGGCTTCGTTTTCGAGAATACCGGCTGCGTCAAGAAAATCCTGGTCAATGGCGCAAGAACCTTCATAGTGCAGGTCCGCATGAGTCACTTTCACGCGGTGGAGTTTGCCCTGCAGCATCGTGCGAATCATAACTTCTACCTTTCTACCCTGTCGTTAACGAAGCAGGCGGTGCCTGCTTTGAGGAAATTCTCACGCAGTATTGCCCGATTTTTGTTTAGTGTCTACTCAT
+>ECs0489
+GAAACCTAAATATTTGTTGTTAAGCTGCAATGGAAACGGTAAAAGCGGCTAGTATTTAAAGGGATGGATGACATCTCAGCGTTGTCGGAGGAGATATTTCATGATGATACGTGAGCGGATAGAAGAAAAATTAAGGGCGGCGTTCCAACCCGTATTCCTCGAAGTAGTGGATGAAAGCTATCGTCACAATGTCCCAGCCGGCTCTGAAAGCCATTTTAAAGTTGTGCTGGTCAGCGATCGTTTTACGGGTGAACGTTTTCTGAATCGTCATCGAATGATTTACAGTACTTTAGCGGAGGAACTCTCTACTACCGTTCATGCGCTGGCTCTGCATACTTACACTATTAAGGAGTGGGAAGGGTTGCAGGACACCGTCTTTGCCTCTCCTCCCTGTCGTGGAGCAGGAAGCATCGCGTAAAAACGCATTTGCAACTGTCGGCGCTTTTCCAGTATGTTGCTAAAGATTTTATGAAAAACGGCCTGCGGGCCGTTTTGTTTTGTCTGGATTTTGCGCTTTT
+>ECs0662
+TCACTTTTTAGTAAAGTTGCACTGGACAAAGCGTACCACAATTGGTGTACTGGTAACCGACACAGCATTTGTGTCTATTTTTCATGTAAAGGTAATTTTGATGTCTAAGATTAAAGGTAACGTTAAGTGGTTTAATGAGTCCAAAGGATTCGGTTTCATTACTCCGGAAGACGGCAGCAAAGACGTGTTCGTACACTTCTCTGCAATCCAGACTAATGGTTTTAAAACTCTTGCTGAAGGTCAGCGCGTAGAGTTCGAAATCACTAACGGTGCCAAAGGCCCTTCTGCTGCAAACGTAATCGCTCTGTAAGATACGTCAGCAAGAATTCAAAACCCGCTTAATCAGCGGGTTTTTTTTGGTCTTTAGTGTGCGGTTGAGGCCGAAAACAGCCAGAATGCCAGTGCGGTCA
+>ECs0916
+TTGTTAATTCGGCGTGAAGAATTGATCCTGGACAGCATTATGCTCAAAAAATAGCCATACTATTTAATTGCAACAAGGCTGGAAAGAGGAGGATCGAAGTATGTTCGTTGACAGACAGCGAATCGATCTGCTGAACCGGTTGATCGACGCACGCGTTGACCTCGCCGCATACGTGCAACTGAGGAAGGCAAAAGGATACATGTCCGTCAGCGAAAGCAATCATCTACGAGATAACTTTTTTAAACTGAATCGCGAACTGCACGATAAATCGCTGCGGTTGAATCTTCATCTGGATCAGGAAGAGTGGAGTGCTCTTCATCATGCTGAAGAAGCATTAGCGACAGCCGCAGTATGTTTGATGAGTGGGCACCATGATTGCCCGACTGTTATTACCGTCAACGCCGATAAGCTTGAAAATTGTCTGATGAGCTTAACGCTGAGTATCCAGAGCCTGCAGAAGCACGCCATGCTTGAGAAGGCCTGAAAACTAAGGGGGAGAAAGCGTCTCCCCCTTCATGTTTAAGTTTTTGTAAAAATGAATTTGTTATCTCCTCCACTGACTACGCTTTAAGCCAGAGTCAATC
+>ECs1050
+TGGTGATGGATCGCTGCCCGGCTATTGAGATCCCTCGCCTGGGCCTGGCCAAATAAAAAATCCCCGGAAGGCAAAAACCTTCCGGGGATCTGTTCAGGGATTAGTTACGCAGACGCGGGGCCTGGAGTTGTTTGCGGATGGTCTGCGCCAGCTCATCCATGGATGGCTGTTCAGGATGTTCATCCTGCAATTCGCTACTTAGCTGGGCTTCAGCCAGGTAGGTATGAACCGGTAGGCCGTTATCGTCCTCCATCACCACGTGATACCACGGAGCGGCGCGAAGCTCGTCATTCACCGCCAGCTCATCAGGCGACGGTTCAGAGAGCGAATAAACCGGGTCGATATCCACGACCACTCCGAGATAACCTAACAGGGAATGGCGGACCTGCTGGCCGATACCGAATTTGCTGGCAATCATAGTCACCTCCCGGGAAATCTTTACCTTTGATATAAGGGTAAAATTCCACATTTCAAGTTACATGACGCGACAGGCAAACCCTTTCAGATATAGCCCTTCC
+>ECs1438
+TCTCATGGTTTAAGCAGAGTAATTAACTGAATGCAGATATACAACCCAGAAATGGTAAAGGCACCGGTGAGGTGCCTTTTGGGTGGATGGTCATGTCATGTTAATGACGCCGATACTCGTTTACCGGGAAATCACCGGATTCAATTTTGGCGATTCCTGCTTCTAATATCGAAATAAATTGTCTGGCAACATCAGTGGTTAACCAGAGCGTCTGACCAACTTCAGTCCCTTCCTGCTCGGACTTATTTGGGGTCTGGTAGTGCAAACGCAACATCAGCGCATCATAGCTATCAACGGTGCTGATGTCCCACCCTACGAGCGGATGAGTCTGAATGACTTCATTATTTTTTTCCATCATGGCCCCCTAATTCGTGTTACTAGACAACGTTATTCGAGGTTCAATGCGTTTTTATCTGAAGCAACTTCAGTATACCAATAAATAAGGGTAATCACCG
+>ECs2085
+TTAACTCCTCAATCCTGTTGCTAGTTTTAAGGACAACATCGCCGTAGCGAAGAAACACGTGCTAAACCCCTAAATTAGGTTGCCGATCAAGCATAGCATCTTAAAGCGTAGGGTGCTGGCCACTGACCACATAATTGATCGTTTGCTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCCACCCATTTGGTCAGCTCCATGAGAATGTCATCTTCAGTGACAACACCGTGCTCTGCCCGAAGGCCTTGCTCAATGGCATTAACCAGAGCGGGTTCTGCTGTTGAATTTTCTGCCTGATAATAAGTAAACATAGTGATTCTCCGTGTCTGTGTATTTATAGTGTCTGCTACGGATCGCAGATTTATAAAGCACATTCAGCATGGCAAATATTTGCCGCTTCGTTGTTAAGAT
+>ECs2384
+ATAAGTGCCTTCCCATCAAAAAAATATTCTCAACATAAAAAACTTTGTGTAATACTTGTAACGCTACATGGAGATTAACTCAATCTAGAGGGTATTAATAATGAAAGCTACTAAACTGGTACTGGGCGCGGTAATCCTGGGTTCTACTCTGCTGGCAGGTTGCTCCAGCAACGCTAAAATCGATCAGCTGTCTTCTGACGTTCAGACTCTGAACGCTAAAGTTGACCAGCTGAGCAACGACGTGAACGCAATGCGTTCCGACGTTCAGGCTGCTAAAGATGACGCAGCTCGTGCTAACCAGCGTCTGGACAACATGGCTACTAAATACCGCAAGTAATAGTACCTGTGAAGTGAAAAATGGCGCACATTGTGCGCCATTTTTTTGTCTGCTATTTACCACTACTGCGTCGCGCGTAACATATTCCCTTGCTCTGGTT
+>ECs2533
+AACGCCAGGAGCGAAGATAAAGCATAGTAAAAAGCCTCGCATTCGACGAGGCTTTATAGCGAGATTGAAGCGTATTCACACTTCAGATCAGTGGATTCGATCAGATAGCTGTTACGTTAACAGCTGCCGGACCTTTCTGGCCGTCCTGAATTTCGAACTCAACGTTCTGACCTTCAGCCAGAGTTTTGAAGCCATTACCCTGGATAGCGGAGAAGTGTACGAACACGTCTTTGCTGCCATCAGCAGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCTTTGCCATTTGAAAAATTCCTTAGATTGTTTTCTTCGCCCGCAGGCATAACATAGATAAAACTGACACATTACTGCATGAGGCACCAATATAAGGCTCGGCAGAGAAG
+>ECs3163
+ACGCCGACGATCGCCGAGACGTTTTCAGACCAGCGCCCACGGGAGAACGCCAGCAGGACGAAGCCAATCAATGGCAAAATAATGGTTAAGGCAAGCATGTTCATCCGCGCATCTCACTTACTGAATCGATGTTCAGGTTCTGGCGACGACGGTGAAGTTGCAGCAGCAGCGCAAGGCCGATACTCGCTTCTGCCGCCGCGAGGCTGATGGCGAGAATGTACATCACCTGACCGTCGGTCTGGCCCCAGTAACTTCCGGCGACCACAAAGGCCAGCGCGGAAGCGTTAATCATGATTTCCAGACCAATCAGCATAAACAGCAGATTGCGACGGATAACCAGACCGGTTAAGCCAAGAACGAATAAGATTGCCGCGAGGATCAGTCCATGTTGTAAGGGGATCATGCGTGCTCCTCCGTTTTTCTTTTCGCGCTGTCGTCTTTACGATTGCTCAGCACTTCACCCGCACGCTCTTCACGACCGACGTGGAAGGCCACAACCAGAC
+>ECs3469
+GCAGTGGTGATTACTCCCCCTTAAAACACGAGCAAACAGATAAAAAAAGGGCCAGCCAATTGGCCAGCCCTTCTTAACAGGATGTCGCTTAAGCGAAATCTTAGTTAAGACGCTCTTTGATACGAGCAGCCTTACCAGTACGCTCACGCAGGTAGTACAGTTTAGCTTTACGAACAGCACCACGACGTTTGACAGAAATGCTGTCAACTACCGGAGAGTGAGTCTGGAAGACACGCTCAACGCCTTCGCCGTTGGAAATTTTACGAACAGTGAATGCAGAGTGCAGACCGCGGTTACGAATAGCGATAACCACGCCCTCGAATGCCTGCAGACGTTTTTTGGAACCTTCAACAACCCATACTTTCACTTCCACGGTATCACCCGGACGGAAGGAAGGTACGTCCTGCTTCATCTGCTCTTGTTCAAGTTGCTTAATAATGTTGCTCATAATTTAATCTCTTATCCTGGGTAAACTGATATCTCGGGGGCTTACGCCATCCCATCATGTTTATGTTGCTGTTGTGCGTGTTCCGTTTTGAACTCCGCCA
+>ECs3602
+GCTTAGGACATTCCGTTTGCATTCGACGGCCAAATCCGGCCGCCGGAACCACGGCGCAAACATCCAAATGAGTGGTTGCCATGTTAATTCCCGGGCTGATTTATCGATTGTTTTGCCCCGCAGACTGTGCGCGCTTCGACGCGTCAGGCACCAGACGATAAAAAGTTTCGCCCGGCCTGGTCATGCTGAGTTCATTACGCGCACGCTCTTCGAGCGCCTCCTGGCCGCCATTGAGATCGTCAATTTCGGCAAAAAGTTGATCGTTTCGCGCTTTAAGTTTCGCGTTTGTAGCTTGCTGTGCCGCCACATCATCATTGACGCGGGTATAGTCATGTATACCGTTCTTACCGAACCACAGCGAATACTGTAGCCAGACCAGAATAGCCAGCAACAGCAGCGTTAGTTTACCCATCCTGCCCCCTGAAAAACGGCATCATCATCCCATGCATCCGAAGACGACTCTACATCCTCTGTTGGGGATACCGCGACAACGCGGGCAAATGTACCACATT
+>ECs4064
+CGGATTAACGTCGCACCATGCGCATTTTTACCGGTTATCGAATGTAAAAAGCCCCGCAACGTGTTGCGGGGCTTTCATCCGTTACCGGGACGCGAAAAACTTATTCAGCTTCGATGCTGATAAATTTACGGTTTTTCGGGCCTTTAACTTCGAATTTCACTTTACCGTCTGCTTTAGCAAACAGAGTGTGGTCACGACCGCAACCTACGTTAGCGCCAGCGTGGAATTTGGTACCACGTTGACGAACGATGATGCTACCCGCCAGAACGGATTCGCCACCGAAACGCTTAACGCCCAGGCGTTTAGCTTCTGAATCGCGACCGTTACGTGTGGAGCCGCCAGCCTTTTTATGTGCCATTTGAAATCTCTCCTCAGGTCTTAGGCGCTGATGCCAGTAATTTTCACATCAGTGAACCACTGACGATGGCCCTGCTGCTTACGATAGTGTTTACGACGAC
+>ECs4440
+GCATGCCCTGACTTCACCCCGCTGTGTCTGCTTTTCCCGACTATTCTTAATGAGCTTCGATGCAATTCACGATCCCGCAGTGTGATTTGAGGAGTTTTCAATGGAATATAAAGATCCAATGCATGAGCTGTTGAGCAGCCTGGAACAGATTGTTTTTAAAGATGAAACGCAGAAAATTACCCTGACGCACAGAACAACGTCCTGTACCGAAATTGAGCAGTTACGAAAAGGGACAGGATTAAAAATCGATGATTTCGCCCGGGTTTTGGGCGTATCAGTCGCCATGGTAAAGGAATGGGAATCCAGACGCGTGAAGCCTTCAAGTGCCGAACTAAAATTGATGCGTTTGATTCAAGCCAACCCGGCATTAAGTAAGCAGTTGATGGAATAGACTTTTATCCACTTTATTGCTGTTTACGGTCCTGATGACAGGACCGTTTTCCAACCGATTAATCATAAATATGAAAAATAATTGTTGCATCACCCGCCAA
+>ECs4714
+TTCTGTTAAATGTGTTTTGCTCATAGTGTGGTAGAATATCAGCTTACTATTGCTTTACGAAAGCGTATCCGGTGAAATAAAGTCAACCTTTAGTTGGTTAATGTTACACCAACAACGAAACCAACACGCCAGGCTTATTCCTGTGGAGTTATATATGAGCGATAAAATTATTCACCTGACTGACGACAGTTTTGACACGGATGTACTCAAAGCGGACGGGGCGATCCTCGTCGATTTCTGGGCAGAGTGGTGCGGTCCGTGCAAAATGATCGCCCCGATTCTGGATGAAATCGCTGACGAATATCAGGGCAAACTGACCGTTGCAAAACTGAACATCGATCAAAACCCTGGCACTGCGCCGAAATATGGCATCCGTGGTATCCCGACTCTGCTGCTGTTCAAAAACGGTGAAGTGGCGGCAACCAAAGTGGGCGCACTGTCTAAAGGTCAGTTGAAAGAGTTCCTCGACGCTAACCTGGCGTAAGGGAATTTCATGTTCGGGTGCCCCGTCGCTAAAAACTGGACGCCCGGCGTGAGTCATGCTAACTTAGTGTTGACTTCGTATTAAACATACCTTATTAAGT
+>ECs4923
+AAAAAGTGGCTATCGGTGCGTGTATGCAGGAGAGTGCTATTCTGGCATTTCCGTCGCACTCGATGCTTAGCAAGCGATAAACACATTGTAAGGATAACTTATGAACAAGACTCAACTGATTGATGTAATTGCAGAGAAAGCAGAACTGTCCAAAACCCAGGCTAAAGCTGCTCTGGAGTCCACTCTGGCTGCAATTACTGAGTCTCTGAAAGAAGGCGATGCTGTACAACTGGTTGGTTTCGGTACCTTCAAAGTGAACCACCGCGCTGAGCGTACTGGCCGCAACCCGCAGACCGGTAAAGAAATCAAAATTGCCGCAGCTAACGTACCGGCATTTGTTTCTGGCAAGGCACTGAAAGACGCAGTTAAGTAAGATTGCGTGGCAGTGAACAGTTTTAACGAAGGGGTGGTTTCACCCCTTTTGTCTTTCTGGCGTCGATCATTGATGCTGGCTGGCGCTCTGTTTCTCACTG
+>ECs5178
+GTTCAGGGGTTCATTTCATGCCACAAGGCAAAGAACGGACTGAGCAAAATGGTTTTGCATGCCGAGCAGATTGAATTGATAGATTCTGGAGACTAGCCATATGGCACGTTATTTCCGTCGTCGCAAGTTCTGCCGTTTCACCGCGGAAGGCGTTCAAGAGATCGACTATAAAGATATCGCTACGCTGAAAAACTACATCACCGAAAGCGGTAAGATTGTCCCAAGCCGTATCACCGGTACCCGTGCAAAATACCAGCGTCAGCTGGCTCGCGCTATCAAACGCGCTCGCTACCTGTCCCTGCTGCCGTACACTGATCGCCATCAGTAATCGGTCACGGTCCATTAATACGACTTTGAGAGGATAAGGTAATGCAAGTTATTCTGCTTGATAAAGTAGCAAACCTGGGTAGCCTGGGTGATCAGGTAAA

modules/trueCoverage_rematch/salmonella_enterica.config

@@ -0,0 +1,20 @@
+#reference_file (fasta file full path)
+/home/mpmachado/INNUca/modules/trueCoverage_rematch/salmonella_enterica.fasta
+#length_extra_seq (int)
+100
+#maximum_number_absent_genes (int)
+2
+#maximum_number_genes_multiple_alleles (int)
+1
+#minimum_read_coverage (x, int)
+25
+#minimum_depth_presence (x, int)
+5
+#minimum_depth_call (x, int)
+10
+#minimum_depth_frequency_dominant_allele (0-1, double)
+0.60
+#minimum_gene_coverage (0-100, int)
+80
+#minimum_gene_identity (0-100, int)
+70