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5. Command line options
Clara Köhne edited this page Jan 23, 2023
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| Option | Description |
|---|---|
--contigs PATH |
Path to one or more nucleotide sequences in FASTA format (required). |
--reference PATH |
Either (1) a path to one or more sequences in FASTA format or (2) a subject database (use --database for the latter; required). |
--database |
When specified, --reference points to a DIAMOND or a BLAST database |
--output-dir PATH |
Write output files to PATH (default path: patchwork_output) |
| Option | Description |
|---|---|
--matrix NAME |
Set the substitution matrix to NAME (default: BLOSUM62) |
--custom-matrix PATH |
Set substitution matrix to the custom matrix in PATH
|
--gapopen NUMBER |
Set the gap open penalty to NUMBER (where NUMBER is a positive integer) |
--gapextend NUMBER |
Set the gap extension penalty to NUMBER (where NUMBER is a positive integer) |
Patchwork supports the following of DIAMOND options:
| Option | Description |
|---|---|
--query-gencode NUMBER |
Set the genetic code. Allowed values can be found on the NCBI website (default: Standard Code) |
--strand STRING |
Set the query strand. Allowed are 'plus', 'minus', and 'both' (default: both) |
--min-orf NUMBER |
Set the minimum open reading frame length |
--fast, --mid-sensitive, --sensitive, --more-sensitive, --very-sensitive, --ultra-sensitive
|
Set the sensitivity mode. You may use at most one flag from the list. If none is provided, the DIAMOND default will be used. |
--iterate [MODE...] |
Iterate through sensitivity settings. For DIAMOND >= 2.0.12, you can optionally specify a list of space-separated sensitivity modes. Allowed values include the above-listed sensitivity values, as well as 'default', and none |
--frameshift NUMBER |
Enable and set penalty for frameshifting operations. Positive integers are allowed |
--evalue NUMBER |
Set e-value cutoff to the specified floating-point number |
--min-score NUMBER |
Set the minimum bitscore threshold (floating-point number). Overrides --evalue
|
--max-target-seqs NUMBER |
Maximum number of subject/reference sequences that are reported per query. Setting to 0 will report all hits (default: 25) |
--top NUMBER |
Report only hits within the given percentage range of the top score. Overrides --max-target-seqs
|
--max-hsps NUMBER |
Maximum number of HSPs DIAMOND may report per target sequence per query. Setting to 0 will report all HSPs (default: 1) |
--id PERCENTAGE |
Report only hits with sequence identity above the given floating-point number |
--query-cover PERCENTAGE |
Discard DIAMOND hits with less query cover than the given percentage |
--subject-cover PERCENTAGE |
Discard DIAMOND hits with less subject cover than the given percentage |
--masking MODE |
Set repeat masking mode. Allowed values are 0 (disabled), 1 (tantan masking) and 2 (BLASTP SEG masking). The last option requires DIAMOND >= 2.0.12. Note that, contrary to the DIAMOND default, Patchwork disables masking by default! (default: 0) |
--len NUMBER |
Discard hits shorter than the provided length |
For a full list of DIAMOND options, see DIAMOND's wiki. If you are missing a flag, please notify us and we can add it to Patchwork's supported DIAMOND options.
The following substitution matrices are available (BLOSUM62 is the default option).
| Matrix | Supported values for (gap open)/(gap extend) | Default gap penalties |
|---|---|---|
| BLOSUM45 | (10-13)/3; (12-16)/2; (16-19)/1 | 14/2 |
| BLOSUM50 | (9-13)/3; (12-16)/2; (15-19)/1 | 13/2 |
| BLOSUM62 | (6-11)/2; (9-13)/1 | 11/1 |
| BLOSUM80 | (6-9)/2; 13/2; 25/2; (9-11)/1 | 10/1 |
| BLOSUM90 | (6-9)/2; (9-11)/1 | 10/1 |
| PAM250 | (11-15)/3; (13-17)/2; (17-21)/1 | 14/2 |
| PAM70 | (6-8)/2; (9-11)/1 | 10/1 |
| PAM30 | (5-7)/2; (8-10)/1 | 9/1 |
If you decide to use a custom matrix, it should adhere to the format used by DIAMOND and BioAlignments.jl. Down below is an example of what such a Matrix could look like:
# Matrix made by matblas from blosum62.iij
# BLOSUM Clustered Scoring Matrix in 1/2 Bit Units
# Blocks Database = /data/blocks_5.0/blocks.dat
# Cluster Percentage: >= 62
# Entropy = 0.6979, Expected = -0.5209
A R N D C Q E G H I L K M F P S T W Y V B Z X
A 4 -1 -2 -2 0 -1 -1 0 -2 -1 -1 -1 -1 -2 -1 1 0 -3 -2 0 -2 -1 0
R -1 5 0 -2 -3 1 0 -2 0 -3 -2 2 -1 -3 -2 -1 -1 -3 -2 -3 -1 0 -1
N -2 0 6 1 -3 0 0 0 1 -3 -3 0 -2 -3 -2 1 0 -4 -2 -3 3 0 -1
D -2 -2 1 6 -3 0 2 -1 -1 -3 -4 -1 -3 -3 -1 0 -1 -4 -3 -3 4 1 -1
C 0 -3 -3 -3 9 -3 -4 -3 -3 -1 -1 -3 -1 -2 -3 -1 -1 -2 -2 -1 -3 -3 -2
Q -1 1 0 0 -3 5 2 -2 0 -3 -2 1 0 -3 -1 0 -1 -2 -1 -2 0 3 -1
E -1 0 0 2 -4 2 5 -2 0 -3 -3 1 -2 -3 -1 0 -1 -3 -2 -2 1 4 -1
G 0 -2 0 -1 -3 -2 -2 6 -2 -4 -4 -2 -3 -3 -2 0 -2 -2 -3 -3 -1 -2 -1
H -2 0 1 -1 -3 0 0 -2 8 -3 -3 -1 -2 -1 -2 -1 -2 -2 2 -3 0 0 -1
I -1 -3 -3 -3 -1 -3 -3 -4 -3 4 2 -3 1 0 -3 -2 -1 -3 -1 3 -3 -3 -1
L -1 -2 -3 -4 -1 -2 -3 -4 -3 2 4 -2 2 0 -3 -2 -1 -2 -1 1 -4 -3 -1
K -1 2 0 -1 -3 1 1 -2 -1 -3 -2 5 -1 -3 -1 0 -1 -3 -2 -2 0 1 -1
M -1 -1 -2 -3 -1 0 -2 -3 -2 1 2 -1 5 0 -2 -1 -1 -1 -1 1 -3 -1 -1
F -2 -3 -3 -3 -2 -3 -3 -3 -1 0 0 -3 0 6 -4 -2 -2 1 3 -1 -3 -3 -1
P -1 -2 -2 -1 -3 -1 -1 -2 -2 -3 -3 -1 -2 -4 7 -1 -1 -4 -3 -2 -2 -1 -2
S 1 -1 1 0 -1 0 0 0 -1 -2 -2 0 -1 -2 -1 4 1 -3 -2 -2 0 0 0
T 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -2 -1 1 5 -2 -2 0 -1 -1 0
W -3 -3 -4 -4 -2 -2 -3 -2 -2 -3 -2 -3 -1 1 -4 -3 -2 11 2 -3 -4 -3 -2
Y -2 -2 -2 -3 -2 -1 -2 -3 2 -1 -1 -2 -1 3 -3 -2 -2 2 7 -1 -3 -2 -1
V 0 -3 -3 -3 -1 -2 -2 -3 -3 3 1 -2 1 -1 -2 -2 0 -3 -1 4 -3 -2 -1
B -2 -1 3 4 -3 0 1 -1 0 -3 -4 0 -3 -3 -2 0 -1 -4 -3 -3 4 1 -1
Z -1 0 0 1 -3 3 4 -2 0 -3 -3 1 -1 -3 -1 0 -1 -3 -2 -2 1 4 -1
X 0 -1 -1 -1 -2 -1 -1 -1 -1 -1 -1 -1 -1 -1 -2 0 0 -2 -1 -1 -1 -1 -1
| Option | Description |
|---|---|
--retain-stops |
Do not remove stop codons (*) in the output sequences |
--retain-ambiguous |
Do not remove ambiguous characters from the output sequences |
--no-trimming |
Disable sliding window alignment trimming |
--window-size NUMBER |
Set the size of the sliding window for alignment trimming (default: 4) |
--required-distance NUMBER |
Set the maximum average distance for the sliding window alignment trimming (default: -7.0) |
| Option | Description |
|---|---|
--threads NUMBER |
The number of threads to utilize in total (default: all available threads) |
--fasta-extension STRING |
Filetype extension for output FASTA files (default: .fas) |
--species-delimiter CHARACTER |
Delimiter used to distinguish the OTU from the rest of the sequence ID in a FASTA header (default: @) |
--no-plots |
Disable plot output to save time |
--wrap-column NUMBER |
Wrap output FASTA sequences the provided column NUMBER (default: no wrap, everything on one line ) |