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Sequence processing

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mothur provides a number of sequence processing commands to go from Sanger sequences or pyrosequences to a distance matrix. These represent a set of tools that will enable you to run a fast and flexible sequence analysis pipeline to enable you to carry out OTU-based approaches and hypothesis testing approaches. Examples of each command are provided within their specific pages, but several users have provided several analysis examples, which use these commands. An exhaustive list of the commands found in mothur is available within the commands category index.

General commands

  • reverse.seqs - output the reverse complement of a sequence collection
  • summary.seqs - summarize a collection of sequences
  • summary.qual - summarize a collection of sequences quality data
  • merge.files - merge two or more sets of files
  • merge.sfffiles - merge two or more sets of sfffiles
  • merge.taxsummary - combines tax summary files.
  • list.seqs - write the sequence names contained within a file to a new file
  • get.seqs - write the data for a sequence name to a new file
  • remove.seqs - remove the data for a sequence name from a new file
  • remove.groups - remove sequence from a specific group or set of groups
  • get.groups - select sequence from a specific group or set of groups
  • split.abund - separate sequences into rare and abundant groups
  • split.groups - separate sequences by group
  • sub.sample - to be used as a way to normalize your data, or create a smaller set from your original set
  • consensus.seqs
  • make.fastq - creates a fastq file from a fasta and quality file
  • deunique.tree - reinserts redundant sequence identifiers into a unique tree
  • count.seqs - counts the number of sequences represented by the representative sequence in a name file.
  • count.groups - counts number of sequences in a group from a shared or group file.
  • sort.seqs - puts sequences in different files in the same order.
  • create.database - creates a database file from a list, repnames, repfasta and contaxonomy file.
  • get.dists - selects distances related to sequences or groups in an accnos file.
  • remove.dists - removes distances related to sequences or groups in an accnos file.

Sequence analysis pipeline

  • sffinfo - extracts sequences from a sff file.
  • trim.flows - trims flowgram data to get ready to run through shhh.flows
  • shhh.flows - the mothur-based re-implementation of PyroNoise
  • make.contigs - create contigs from forward and reverse fastq files.
  • shhh.seqs - a mothur-based rewrite of Chris Quince's sequence denoising program, SeqNoise
  • fastq.info - parses fastq file into fasta and quality files
  • trim.seqs - pre-process sequences to remove primers, generate group file, and screen for quality
  • unique.seqs - identify the unique sequences in a collection and generate a names file
  • deunique.seqs - reverse unique.seqs
  • pre.cluster - implements a pseudo-single linkage algorithm with the goal of removing sequences that are likely due to pyrosequencing errors
  • cluster.fragments - clusters sequences that are fragments of a larger sequence
  • chop.seqs -
  • align.seqs - align sequences against a reference alignment
  • filter.seqs - filter positions out of an alignment
  • screen.seqs - remove sequences that don't satisfy criteria
  • seq.error - a function that assesses error rates in sequencing data
  • chimera.bellerophon - identify potentially chimeric sequences
  • chimera.check - identify potentially chimeric sequences
  • chimera.ccode - identify potentially chimeric sequences
  • chimera.pintail - identify potentially chimeric sequences
  • chimera.slayer - identify potentially chimeric sequences
  • chimera.uchime - identify potentially chimeric sequences
  • chimera.perseus - identify potentially chimeric sequences
  • align.check - characterize the alignment quality for 16S rRNA gene sequences
  • dist.seqs - generate a pairwise distance matrix
  • pairwise.seqs - generate a pairwise distance matrix
  • pcr.seqs - trim inputted sequences based on a variety of user-defined options
  • primer.design - will generate candidate PCR primers for OTUs of interest