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comparison 0.3.0/readme/centriflaken_hy.md @ 97:8d7f482c64de

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author kkonganti
date Fri, 29 Jul 2022 11:11:07 -0400
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13 `centriflaken_hy` is a variant of the original `centriflaken` pipeline but for Illumina short reads either single-end or paired-end. 13 `centriflaken_hy` is a variant of the original `centriflaken` pipeline but for Illumina short reads either single-end or paired-end.
14 14
15 #### Workflow Usage 15 #### Workflow Usage
16 16
17 ```bash 17 ```bash
18 module load cpipes/0.2.1 18 module load cpipes/0.3.0
19 19
20 cpipes --pipeline centriflaken_hy [options] 20 cpipes --pipeline centriflaken_hy [options]
21 ``` 21 ```
22 22
23 Example: Run the default `centriflaken_hy` pipeline with taxa of interest as *E. coli*. 23 Example: Run the default `centriflaken_hy` pipeline with taxa of interest as *E. coli*.
41 #### `centriflaken_hy` Help 41 #### `centriflaken_hy` Help
42 42
43 ```text 43 ```text
44 [Kranti.Konganti@login2-slurm ]$ cpipes --pipeline centriflaken_hy --help 44 [Kranti.Konganti@login2-slurm ]$ cpipes --pipeline centriflaken_hy --help
45 N E X T F L O W ~ version 21.12.1-edge 45 N E X T F L O W ~ version 21.12.1-edge
46 Launching `/nfs/software/apps/cpipes/0.2.1/cpipes` [wise_noyce] - revision: 72db279311 46 Launching `/home/Kranti.Konganti/apps/cpipes/cpipes` [condescending_jang] - revision: 72db279311
47 ================================================================================ 47 ================================================================================
48 (o) 48 (o)
49 ___ _ __ _ _ __ ___ ___ 49 ___ _ __ _ _ __ ___ ___
50 / __|| '_ \ | || '_ \ / _ \/ __| 50 / __|| '_ \ | || '_ \ / _ \/ __|
51 | (__ | |_) || || |_) || __/\__ \ 51 | (__ | |_) || || |_) || __/\__ \
55 -------------------------------------------------------------------------------- 55 --------------------------------------------------------------------------------
56 A collection of modular pipelines at CFSAN, FDA. 56 A collection of modular pipelines at CFSAN, FDA.
57 -------------------------------------------------------------------------------- 57 --------------------------------------------------------------------------------
58 Name : CPIPES 58 Name : CPIPES
59 Author : Kranti.Konganti@fda.hhs.gov 59 Author : Kranti.Konganti@fda.hhs.gov
60 Version : 0.2.1 60 Version : 0.3.0
61 Center : CFSAN, FDA. 61 Center : CFSAN, FDA.
62 ================================================================================ 62 ================================================================================
63 63
64 Workflow : centriflaken_hy 64 Workflow : centriflaken_hy
65 65
66 Author : Kranti.Konganti@fda.hhs.gov 66 Author : Kranti.Konganti@fda.hhs.gov
67 67
68 Version : 0.2.0 68 Version : 0.3.0
69 69
70 70
71 Usage : cpipes --pipeline centriflaken_hy [options] 71 Usage : cpipes --pipeline centriflaken_hy [options]
72 72
73 73
174 Default: Escherichia coli 174 Default: Escherichia coli
175 175
176 --centrifuge_ignore_quals : Treat all quality values as 30 on Phred 176 --centrifuge_ignore_quals : Treat all quality values as 30 on Phred
177 scale. Default: false 177 scale. Default: false
178 178
179 --megahit_run : Run MEGAHIT assembler. Default: true
180
181 --megahit_min_count : <int>. Minimum multiplicity for filtering (
182 k_min+1)-mers. Defaut: false
183
184 --megahit_k_list : Comma-separated list of kmer size. All
185 values must be odd, in the range 15-255,
186 increment should be <= 28. Ex: '21,29,39,59,
187 79,99,119,141'. Default: false
188
189 --megahit_no_mercy : Do not add mercy k-mers. Default: false
190
191 --megahit_bubble_level : <int>. Intensity of bubble merging (0-2), 0
192 to disable. Default: false
193
194 --megahit_merge_level : <l,s>. Merge complex bubbles of length <= l*
195 kmer_size and similarity >= s. Default:
196 false
197
198 --megahit_prune_level : <int>. Strength of low depth pruning (0-3).
199 Default: false
200
201 --megahit_prune_depth : <int>. Remove unitigs with avg k-mer depth
202 less than this value. Default: false
203
204 --megahit_low_local_ratio : <float>. Ratio threshold to define low
205 local coverage contigs. Default: false
206
207 --megahit_max_tip_len : <int>. remove tips less than this value [<
208 int> * k]. Default: false
209
210 --megahit_no_local : Disable local assembly. Default: false
211
212 --megahit_kmin_1pass : Use 1pass mode to build SdBG of k_min.
213 Default: false
214
215 --megahit_preset : <str>. Override a group of parameters.
216 Valid values are meta-sensitive which
217 enforces '--min-count 1 --k-list 21,29,39,
218 49,...,129,141', meta-large (large &
219 complex metagenomes, like soil) which
220 enforces '--k-min 27 --k-max 127 --k-step
221 10'. Default: meta-sensitive
222
223 --megahit_mem_flag : <int>. SdBG builder memory mode. 0: minimum;
224 1: moderate; 2: use all memory specified.
225 Default: 2
226
227 --megahit_min_contig_len : <int>. Minimum length of contigs to output.
228 Default: false
229
230 --spades_run : Run SPAdes assembler. Default: false
231
179 --spades_isolate : This flag is highly recommended for high- 232 --spades_isolate : This flag is highly recommended for high-
180 coverage isolate and multi-cell data. 233 coverage isolate and multi-cell data.
181 Defaut: false 234 Defaut: false
182 235
183 --spades_sc : This flag is required for MDA (single-cell) 236 --spades_sc : This flag is required for MDA (single-cell)
210 263
211 --spades_iontorrent : This flag is required for IonTorrent data. 264 --spades_iontorrent : This flag is required for IonTorrent data.
212 Default: false 265 Default: false
213 266
214 --spades_only_assembler : Runs only the SPAdes assembler module ( 267 --spades_only_assembler : Runs only the SPAdes assembler module (
215 without read error correction).Default: 268 without read error correction). Default:
216 false 269 false
217 270
218 --spades_careful : Tries to reduce the number of mismatches 271 --spades_careful : Tries to reduce the number of mismatches
219 and short indels in the assembly. Default: 272 and short indels in the assembly. Default:
220 false 273 false