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1 # bettercallsal_db
2
3 `bettercallsal_db` is an end-to-end automated workflow to generate and consolidate the required DB flat files based on [NCBI Pathogens Database for Salmonella](https://ftp.ncbi.nlm.nih.gov/pathogen/Results/Salmonella/). It first downloads the metadata based on the provided release identifier (Ex: `latest_snps` or `PDG000000002.3082`) and then creates a `mash sketch` based on the filtering strategy. It generates two types of sketches, one that prioritizes genome collection based on SNP clustering (`per_snp_cluster`) and the other just collects up to N number of genome accessions for each `computed_serotype` column from the metadata file (`per_computed_serotype`).
4
5 The `bettercallsal_db` workflow should finish within an hour with stable internet connection.
6
7 \
8  
9
10 ## Workflow Usage
11
12 ```bash
13 cpipes --pipeline bettercallsal_db [options]
14 ```
15
16 \
17  
18
19 Example: Run the `bettercallsal_db` pipeline and store output at `/data/Kranti_Konganti/bettercallsal_db/PDG000000002.3082`.
20
21 ```bash
22 cpipes
23 --pipeline bettercallsal_db \
24 --pdg_release PDG000000002.3082 \
25 --output /data/Kranti_Konganti/bettercallsal_db/PDG000000002.3082
26 ```
27
28 \
29  
30
31 Now you can run the `bettercallsal` workflow with the created database by mentioning the root path to the database with `--bcs_root_dbdir` option.
32
33 ```bash
34 cpipes
35 --pipeline bettercallsal \
36 --input /path/to/illumina/fastq/dir \
37 --output /path/to/output \
38 --bcs_root_dbdir /data/Kranti_Konganti/bettercallsal_db/PDG000000002.3082
39 ```
40
41 \
42  
43
44 ## Note
45
46 Please note that the last step of the `bettercallsal_db` workflow named `SCAFFOLD_GENOMES` will spawn multiple processes and is not cached by **Nextflow**. This is an intentional setup for this specific stage of the workflow to speed up database creation and as such it is recommended that you run this workflow in a grid computing or similar cloud computing setting.
47
48 \
49  
50
51 ## `bettercallsal_db` CLI Help
52
53 ```text
54 [Kranti_Konganti@my-unix-box ]$ cpipes --pipeline bettercallsal_db --help
55
56 N E X T F L O W ~ version 24.04.3
57
58 Launching `~/apps/bettercallsal/1.0.0/cpipes` [shrivelled_hamilton] DSL2 - revision: d9b4be42be
59
60 ================================================================================
61 (o)
62 ___ _ __ _ _ __ ___ ___
63 / __|| '_ \ | || '_ \ / _ \/ __|
64 | (__ | |_) || || |_) || __/\__ \
65 \___|| .__/ |_|| .__/ \___||___/
66 | | | |
67 |_| |_|
68 --------------------------------------------------------------------------------
69 A collection of modular pipelines at CFSAN, FDA.
70 --------------------------------------------------------------------------------
71 Name : bettercallsal
72 Author : Kranti Konganti
73 Version : 0.9.0
74 Center : CFSAN, FDA.
75 ================================================================================
76
77 Workflow : bettercallsal_db
78
79 Author : Kranti Konganti
80
81 Version : 1.0.0
82
83
84 Required :
85
86 --output : Absolute path to directory where all the
87 pipeline outputs should be stored. Ex: --
88 output /path/to/output
89
90 Other options :
91
92 --wcomp_serocol : Column number (non 0-based index) of the
93 PDG metadata file by which the serotypes
94 are collected. Default: false
95
96 --wcomp_seronamecol : Column number (non 0-based index) of the
97 PDG metadata file whose column name is "
98 serovar". Default: false
99
100 --wcomp_acc_col : Column number (non 0-based index) of the
101 PDG metadata file whose column name is "acc
102 ". Default: false
103
104 --wcomp_target_acc_col : Column number (non 0-based index) of the
105 PDG metadata file whose column name is "
106 target_acc". Default: false
107
108 --wcomp_complete_sero : Skip indexing serotypes when the serotype
109 name in the column number 49 (non 0-based)
110 of PDG metadata file consists a "-". For
111 example, if an accession has a serotype=
112 string as such in column number 49 (non 0-
113 based): "serotype=- 13:z4,z23:-" then, the
114 indexing of that accession is skipped.
115 Default: false
116
117 --wcomp_not_null_serovar : Only index the computed_serotype column i.e
118 . column number 49 (non 0-based), if the
119 serovar column is not NULL. Default: false
120
121 --wcomp_i : Force include this serovar. Ignores --
122 wcomp_complete_sero for only this serovar.
123 Mention multiple serovars separated by a
124 ! (Exclamation mark). Ex: --
125 wcomp_complete_sero I 4,[5],12:i:-!Agona
126 Default: false
127
128 --wcomp_num : Number of genome accessions to be collected
129 per serotype. Default: false
130
131 --wcomp_min_contig_size : Minimum contig size to consider a genome
132 for indexing. Default: false
133
134 --wsnp_serocol : Column number (non 0-based index) of the
135 PDG metadata file by which the serotypes
136 are collected. Default: false
137
138 --wsnp_seronamecol : Column number (non 0-based index) of the
139 PDG metadata file whose column name is "
140 serovar". Default: false
141
142 --wsnp_acc_col : Column number (non 0-based index) of the
143 PDG metadata file whose column name is "acc
144 ". Default: false
145
146 --wsnp_target_acc_col : Column number (non 0-based index) of the
147 PDG metadata file whose column name is "
148 target_acc". Default: false
149
150 --wsnp_complete_sero : Skip indexing serotypes when the serotype
151 name in the column number 49 (non 0-based)
152 of PDG metadata file consists a "-". For
153 example, if an accession has a serotype=
154 string as such in column number 49 (non 0-
155 based): "serotype=- 13:z4,z23:-" then, the
156 indexing of that accession is skipped.
157 Default: true
158
159 --wsnp_not_null_serovar : Only index the computed_serotype column i.e
160 . column number 49 (non 0-based), if the
161 serovar column is not NULL. Default: false
162
163 --wsnp_i : Force include this serovar. Ignores --
164 wsnp_complete_sero for only this serovar.
165 Mention multiple serovars separated by a
166 ! (Exclamation mark). Ex: --
167 wsnp_complete_sero I 4,[5],12:i:-!Agona
168 Default: 'I 4,[5],12:i
169
170 --wsnp_num : Number of genome accessions to collect per
171 SNP cluster. Default: false
172
173 --mashsketch_run : Run `mash screen` tool. Default: true
174
175 --mashsketch_l : List input. Lines in each <input> specify
176 paths to sequence files, one per line.
177 Default: true
178
179 --mashsketch_I : <path> ID field for sketch of reads (
180 instead of first sequence ID). Default:
181 false
182
183 --mashsketch_C : <path> Comment for a sketch of reads (
184 instead of first sequence comment). Default
185 : false
186
187 --mashsketch_k : <int> K-mer size. Hashes will be based on
188 strings of this many nucleotides.
189 Canonical nucleotides are used by default (
190 see Alphabet options below). (1-32) Default
191 : 21
192
193 --mashsketch_s : <int> Sketch size. Each sketch will have
194 at most this many non-redundant min-hashes
195 . Default: 1000
196
197 --mashsketch_i : Sketch individual sequences, rather than
198 whole files, e.g. for multi-fastas of
199 single-chromosome genomes or pair-wise gene
200 comparisons. Default: false
201
202 --mashsketch_S : <int> Seed to provide to the hash
203 function. (0-4294967296) [42] Default:
204 false
205
206 --mashsketch_w : <num> Probability threshold for warning
207 about low k-mer size. (0-1) Default: false
208
209 --mashsketch_r : Input is a read set. See Reads options
210 below. Incompatible with --mashsketch_i.
211 Default: false
212
213 --mashsketch_b : <size> Use a Bloom filter of this size (
214 raw bytes or with K/M/G/T) to filter out
215 unique k-mers. This is useful if exact
216 filtering with --mashsketch_m uses too much
217 memory. However, some unique k-mers may
218 pass erroneously, and copies cannot be
219 counted beyond 2. Implies --mashsketch_r.
220 Default: false
221
222 --mashsketch_m : <int> Minimum copies of each k-mer
223 required to pass noise filter for reads.
224 Implies --mashsketch_r. Default: false
225
226 --mashsketch_c : <num> Target coverage. Sketching will
227 conclude if this coverage is reached before
228 the end of the input file (estimated by
229 average k-mer multiplicity). Implies --
230 mashsketch_r. Default: false
231
232 --mashsketch_g : <size> Genome size (raw bases or with K/M/
233 G/T). If specified, will be used for p-
234 value calculation instead of an estimated
235 size from k-mer content. Implies --
236 mashsketch_r. Default: false
237
238 --mashsketch_n : Preserve strand (by default, strand is
239 ignored by using canonical DNA k-mers,
240 which are alphabetical minima of forward-
241 reverse pairs). Implied if an alphabet is
242 specified with --mashsketch_a or --
243 mashsketch_z. Default: false
244
245 --mashsketch_a : Use amino acid alphabet (A-Z, except BJOUXZ
246 ). Implies --mashsketch_n --mashsketch_k 9
247 . Default: false
248
249 --mashsketch_z : <text> Alphabet to base hashes on (case
250 ignored by default; see --mashsketch_Z). K-
251 mers with other characters will be ignored
252 . Implies --mashsketch_n. Default: false
253
254 --mashsketch_Z : Preserve case in k-mers and alphabet (case
255 is ignored by default). Sequence letters
256 whose case is not in the current alphabet
257 will be skipped when sketching. Default:
258 false
259
260 Help options :
261
262 --help : Display this message.
263
264 ```