# list.seqs

The list.seqs command will write out the names of the sequences found within a fastq, fasta, name, group, count, list, qfile, or align.report file. This could be useful for using the get.seqs and remove.seqs commands as well as to generate a group file. To complete this analysis, you need to download the folder compressed in the Esophagus.zip archive.

## Options

At least one of the following options must be used. Each of these options will generate a file ending in accnos that contains a single column containing the list of the sequences contained in the input files.

### fastq option

The fastq option is used as presented in the following command:

mothur > list.seqs(fastq=test.fastq)


You can enter multiple files separated by ‘-‘’s and mothur will output an accnos file containing reads present in all files. This can be helpful when correcting file mismatches. For example if you have missing reads in your paired fastq files, try this:

mothur > list.seqs(fastq=test.R1.fastq-test.R2.fastq)
mothur > get.seqs(fastq=test.R1.fastq-test.R2.fastq, accnos=current)


Mothur can also read compressed files as inputs:

mothur > list.seqs(fastq=test.R1.fastq.gz-test.R2.fastq.gz)


### fasta option

The fasta option is used as presented in the following command:

mothur > list.seqs(fasta=esophagus.fasta)


The resulting esophagus.accnos file looks something like:

59_10_1
59_10_10
59_10_11
59_10_13
59_10_15
59_10_16
59_10_17
...


You can enter multiple files separated by ‘-‘’s and mothur will output an accnos file containing reads present in all files. For example if you want to know what reads are common to several samples, try this:

mothur > split.groups(fasta=test.fasta, count=test.count_table) - creates a fasta and count table for each sample
mothur > list.seqs(fasta=test.sample1.fasta-test.sample2.fasta-test.sample3.fasta) - lists sequences present in sample1, sample2 and sample3


### count option

The count file is similar to the name file in that it is used to represent the number of duplicate sequences for a given representative sequence. It can also contain group information.

mothur > list.seqs(count=esophagus.count_table)


You can enter multiple files separated by ‘-‘’s and mothur will output an accnos file containing reads present in all files.

### alignreport option

The alignreport option is used as presented in the following command:

mothur > list.seqs(alignreport=esophagus.align.report)


### list option

The list option is used as presented in the following command:

mothur > list.seqs(list=esophagus.fn.list)


You can enter multiple files separated by ‘-‘’s and mothur will output an accnos file containing reads present in all files.

### taxonomy option

The taxonomy option is used as presented in the following command:

mothur > list.seqs(taxonomy=esophagus.silva.full.taxonomy)


You can enter multiple files separated by ‘-‘’s and mothur will output an accnos file containing reads present in all files.

mothur > list.seqs(fasta=final.fasta, count=final.count_table, taxonomy=final.taxonomy)
mothur > get.seqs(fasta=final.fasta, count=final.count_table, taxonomy=final.taxonomy, accnos=current)


### qfile option

The qfile option allows you to include a quality file. This can be helpful when correcting file mismatches between fasta and quality files. Mothur will output an accnos file containing the sequences present in both the fasta and quality file.

mothur > list.seqs(qfile=test.qual, fasta=test.fasta)
mothur > get.seqs(qfile=current, fasta=current, accnos=current)


The name option allows you to provide a name file.

We DO NOT recommend using the name file. Instead we recommend using a count file. The count file reduces the time and resources needed to process commands. It is a smaller file and can contain group information.

The group parameter allows you to provide a group file.

We DO NOT recommend using the name / group file combination. Instead we recommend using a count file. The count file reduces the time and resources needed to process commands. It is a smaller file and can contain group information.