Consed Current Features

• Supports mixtures of all types of reads of any lengths: Illumina, Sanger, 454, downloaded reference sequences, etc.
• BamView features:
  1. Shows read depth and depth of reads with inconsistently mapped mate pairs
  2. Shows % of reads discrepant at each position
  3. Allows bringing up consed on a targetted location
• Bam2Ace will convert part or all of a bam file to a consed-ready format
• consed -shallowerDepth will take a high depth of coverage assembly and make a shallow depth of coverage assembly while preserving alleles and (optionally) mate pairs
• Shows overview of the assembly showing:
  1. read depth
  2. density of variants (substitutions and indels shown separately)
  3. tags (you can choose which types of tags to see)
  4. how contigs are ordered and oriented due to forward-reverse pair data
  5. which forward-reverse pairs that are consistent and which are inconsistent with the assembly, thus showing points of likely misassembly. Optionally, can pop up the read bases aligned against the consensus.
  6. internal sequence matches which can be filtered in many different ways. Optionally can see alignment.
  7. forward/reverse pair depth
  8. restriction digest cut sites
• Can add reads in Consed without reassembling
• Can fix the consensus in batch
• Can fix the consensus and alignments of reads near the ends of the contigs
• Edit Operations:
  1. change a base call, insert a base call, delete a base call
  2. change a consensus base
  3. add a tag either to a read or to the consensus. Note: consensus tags will still be there after reassembling
• Undo edit (one or many)
• Traces from several reads (or all reads) can be viewed simultaneously. They are kept aligned as you scroll. The contig and the traces are kept in corresponding locations.
• Has a Quick Tour of Consed to easily and quickly take you through a demonstration of all of Consed's features in less than 5 hours
• Can try various alignments of regions from 2 different contigs and make joins
• Can find and make joins in a fully or semi-automated manner
• Can tear in contig in two
• Can move a single read from one location to another
• Can reassemble (using phrap) just a particular region
• Picks primers and templates for whichever location you specify
• Picks PCR primer pairs
• Keeps a log of all user performed manipulations of the assembly
• Can reassemble after editing and your edits will be used by Phrap
• Move automatically to next problem area (saves wading through kilobases looking for problem areas) Problem areas are defined in various ways:
  1. a position in which multiple reads disagree with the reference sequence
  2. a consensus region that has too high an error probability
  3. a base that has a very low error probability but that disagrees with the reference sequence
  4. a region that is single stranded and single chemistry
  5. a region that is only covered by a single subclone
  6. a stretch of a read that has a very low error probability, but disagrees with the consensus so much that it cannot be aligned
  7. a location specified by a custom user-created file
  8. a location in which multiple reads all have the same high quality discrepancy (possibly indicates a collapsed repeat or a SNP)
  (These have configurable thresholds.)
  
• Shows regions of reads that have significant matches elsewhere in the assembly
• Button to instantly switch meaning of color:
  • Greyscale indicates quality and colored of part of base indicates tag (sequence annotation)
  • Color indicates match/mismatch with the consensus
  • Color indicates whether base was edited or not
• Ability to fix a read (or reads) at the top of the Aligned Reads Window...handy for following a particular read
• Parameters can be modified either for editing session or for all future sessions. Can be modified just for a user, just for a project, or for all users and all projects.
• Can complement a contig
• Can hide specific tags (to avoid clutter)
• Can add a read name to a file with one click (convenient for many purposes). Can also add notes along with the read name.
• Can back out edits to a particular read
• Can remove some reads from an assembly
• Can show the numeric quality value (error probability) of a read or consensus base
• Can dim the low quality and/or unaligned beginning and ends of reads
• Can search for a string of bases (exactly or approximately) and click to go to any of the hits
• Can compare a real restriction digest gel to a gel predicted from the sequence.
• Consed includes Autofinish which will automatically choose finishing reads, speeding up finishing and making it cheaper. (See below for success data on Autofinish and also see Genome Research, April 2001 for a paper on Autofinish.)
• Some operations can be run by a script (not interactively) so they can be done a large number of times without a person needing to tediously perform them. For example:
  • Picking PCR primers to amplify regions
  • Adding new reads to assemblies
  • Tagging regions for various reasons, such as if a base is editable
• Viewing and editing 454 reads
• Many other features