q2-pepsirf: A QIIME 2 plugin for the pep_sirf software package
The pep_sirf package must first be installed and built, and the executable must be accessible by calling 'pep_sirf' from your command-line environment. The best way to do this would be to put the pep_sirf executable somewhere located in your $PATH.
Clone this repo and enter the q2-pepsirf directory.
Then, activate your qiime2 conda environment and run
python3 setup.py install
qiime dev refresh-cache
The plugin should now be available from qiime.
Usage: qiime pepsirf demux [OPTIONS]
Description
Inputs:
--i-reads ARTIFACT MultiplexedSingleEndBarcodeInSequence
Input reads file to parse. These should be in fastq
format. Reads can already be indexed on the reverse
barcode sequences, in which case the r-index
parameter should not be specified. If the reverse
barcodes are in the reads the r-index parameter
should be specified. If you have one file for
forward reads and one for reverse reads the
demux_paired command should be used. [required]
--i-library ARTIFACT FeatureData[Sequence]
Designed library containing nucleic acidpeptides.
Library should be in fasta format and should contain
sequences thatwere used to design the sequences in
reads. [required]
--i-barcodes ARTIFACT FeatureData[Sequence]
Name of fasta file containing forward and
(potentially) reverse barcode sequences. [required]
Parameters:
--p-samplelist TEXT A tab-delimited list of samples, one sample per
line. If the samples are already indexed by I2 only
the forward index (I1) and the sample name are
required. The first item in each tab-delimited line
is the forward (I1) index, the second (if included)
is the reverse (I2) index, and the third is the
sample name. [required]
--p-f-index TEXT Positional values for f-index. This argument must
be passed as 3 comma-separated values. The first
item represents the (0-based) expected start index
of the forward index. The second represents the
length of the forward index, and the third
represents the number of mismatches that are
tolerated for this index. An example is
"--f_index12,12,2". This says that we start at
(0-based) index 12, grab the next 12 characters, and
if a perfect match is not found for these grabbed
characters we look for a match to the forward
indexsequences with up to two allowed mismatches.
[required]
--p-seq TEXT Positional values for nucleotide sequence data.
This argument must be passed as 3 comma-separated
values. The first item represents the (0-based)
expected start index of the sequence. The second
represents the length of the sequence, and the third
represents the number of mismatches that are
tolerated for a sequence. An example is "--seq
43,90,2". This says that we start at (0-based) index
43, grab the next 90 characters, and if a perfect
match is not found for these grabbed characters we
look for a match to the designed library sequences
with up to two allowedmismatches. [required]
--p-r-index TEXT Positional values for r-index. This argument must
be passed as 3 comma-separated values. The first
item represents the (0-based) expected start index
of the reverse index. The second represents the
length of the reverse index, and the third
represents the number of mismatches that are
tolerated for this index. An example is
"--r_index12,12,2". This says that we start at
(0-based) index 12, grab the next 12 characters, and
if a perfect match is not found for these grabbed
characters we look for a match to the reverse
indexsequences with up to two allowed mismatches.
[default: '']
--p-num-threads INTEGER The number of threads to use for analyses
[default: 2]
--p-read-per-loop INTEGER
The number of fastq records read a time.A higher
value will result in more memory usage by the
program, but will also result in fewer disk
accesses, increasing performance of the program.
[default: 800000]
--p-concatemer TEXT Concatenated primer sequences. If this concatemer
is found within a read, we know that a potential
sequence from the designed library was not included.
The number of times this concatemer is recorded in
the input file is reported. [default: '']
--p-aa-counts TEXT [default: '']
Outputs:
--o-nt-counts ARTIFACT FeatureTable[Frequency]
[required]
--o-aa-counts-o ARTIFACT FeatureTable[Frequency]
[required]
Miscellaneous:
--output-dir PATH Output unspecified results to a directory
--verbose / --quiet Display verbose output to stdout and/or stderr
during execution of this action. Or silence output
if execution is successful (silence is golden).
--citations Show citations and exit.
--help Show this message and exit.
Demultiplex paired-end reads, where the second read can be either a file containing only reverse indexes or reverse reads.
Usage: qiime pepsirf demux-paired [OPTIONS]
Description
Inputs:
--i-f-reads ARTIFACT MultiplexedSingleEndBarcodeInSequence
Input reads file to parse. [required]
--i-r-reads ARTIFACT MultiplexedSingleEndBarcodeInSequence
Input reverse reads file to parse. This file can
contain either just barcode reads or contain reverse
reads. Either way the expected position of the
reverse barcodes must be specified by the r-index
parameter. [required]
--i-library ARTIFACT FeatureData[Sequence]
Designed library containing nucleic acidpeptides.
Library should be in fasta format and should contain
sequences thatwere used to design the sequences in
reads. [required]
--i-barcodes ARTIFACT FeatureData[Sequence]
Name of fasta file containing forward and
(potentially) reverse barcode sequences. [required]
Parameters:
--p-samplelist TEXT A tab-delimited list of samples, one sample per
line. If the samples are already indexed by I2 only
the forward index (I1) and the sample name are
required. The first item in each tab-delimited line
is the forward (I1) index, the second (if included)
is the reverse (I2) index, and the third is
thesamplename. [required]
--p-seq TEXT Positional values for nucleotide sequence data.
This argument must be passed as 3 comma-separated
values. The first item represents the (0-based)
expected start index of the sequence. The second
represents the length of the sequence, and the third
represents the number of mismatches that are
tolerated for a sequence. An example is "--seq
43,90,2". This says that we start at (0-based) index
43, grab the next 90 characters, and if a perfect
match is not found for these grabbed characters we
look for a match to the designed library sequences
with up to two allowedmismatches. [required]
--p-f-index TEXT Positional values for f-index. This argument must
be passed as 3 comma-separated values. The first
item represents the (0-based) expected start index
of the forward index. The second represents the
length of the forward index, and the third
represents the number of mismatches that are
tolerated for this index. An example is
"--f_index12,12,2". This says that we start at
(0-based) index 12, grab the next 12 characters, and
if a perfect match is not found for these grabbed
characters we look for a match to the forward
indexsequences with up to two allowed mismatches.
[required]
--p-r-index TEXT Positional values for r-index. This argument must
be passed as 3 comma-separated values. The first
item represents the (0-based) expected start index
of the reverse index. The second represents the
length of the reverse index, and the third
represents the number of mismatches that are
tolerated for this index. An example is
"--r_index12,12,2". This says that we start at
(0-based) index 12, grab the next 12 characters, and
if a perfect match is not found for these grabbed
characters we look for a match to the reverse
indexsequences with up to two allowed mismatches.
[default: '']
--p-num-threads INTEGER The number of threads to use for analyses
[default: 2]
--p-read-per-loop INTEGER
The number of fastq records read a time.A higher
value will result in more memory usage by the
program, but will also result in fewer disk
accesses, increasing performance of the program.
[default: 800000]
--p-concatemer TEXT Concatenated primer sequences. If this concatemer
is found within a read, we know that a potential
sequence from the designed library was not included.
The number of times this concatemer is recorded in
the input file is reported. [default: '']
--p-aa-counts TEXT [default: '']
Outputs:
--o-nt-counts ARTIFACT FeatureTable[Frequency]
[required]
--o-aa-counts-o ARTIFACT FeatureTable[Frequency]
[required]
Miscellaneous:
--output-dir PATH Output unspecified results to a directory
--verbose / --quiet Display verbose output to stdout and/or stderr
during execution of this action. Or silence output
if execution is successful (silence is golden).
--citations Show citations and exit.
--help Show this message and exit.