Updates

Latest updates:

  1. Sep 2020 - Fixed bug when twoBitToFa sometimes fetches whole chromosome instead of 1bp position, added --noOverlapping option and forced it on website users who search for nanopore enrichment (large area, relaxed off-target requirements) and isoform targetting (permissive PAM results in a lot of unnecessary overlaps).
  2. Jun 2019 - Fixed bug when restricting to 3' UTR, fixed ensemble identifiers for the mm10 genome, updated hg38 to latest gencode supported by the ucsc, small fixes for the website
  3. Dec 30 2018 Release of CHOPCHOP version 3.0.0
    1. Support for isoform targeting with CRISPR/Cas13
    2. Support for no PAM targeting
    3. Intersection/Union of isoforms when user specifies gene with multiple isoforms
    4. Display of multiple isoforms as well as IN FRAME downstream ATG sites
    5. Support for nanopore enrichment
    6. Precise analysis and testing of our alignment algorithm with bowtie, compared with other approaches. Only bowtie (up to 3 mismatches), cas-offinder
      7. and scan_for_matches (up to 6 mismatches) are able to pass our tests with precision and accuracy. Bowtie2, bwa, vmatch seem to be imprecise, at least when using alignment strategies from other crispr designing software. Only bowtie is able to support searches for offtargets with up to 3 mismatches without any errors, as well as supports early stopping (there is no value in searching all off-targets above first k reported), therefore we continue using bowtie for off-target finding. Value of k can be adjusted in python CHOPCHOP, on the website it is set to 300 (200 for TALENs).
    7. We have grown database of organisms to 162.
    8. Specific presets for less advanced users that will not require complete reading of CHOPCHOP options.
    9. Scripts for batch targeting of multiple genes, and design of control guides.
    10. Complete new website that will be able to handle all the traffic from you!
  4. Dec 3 2018 - Updated CHO-K1 genome with an assembly with gene IDs (GCF_000223135.1/CriGri_1.0). Example gene ID: XM_007607631.2
  5. Dec 3 2018 - Simplified the Solanum lycopersicum (SL3.0) gene IDs by removing the period and subsequent number. E.g. Solyc03g115850.3 is now Solyc03g115850
  6. Aug 22 2018 - Fixed a bug where off-targets with 3 mismatches were not always found. CHOPCHOP is now able to find ALL off-targets with up to 3 mismatches, but we decided to use early stopping ('>=' sign indicates that there exist potentially even more mismatches than reported). Early stopping is only used when there is more than k (300 for CRISPR, 200 for TALEN) off-targets already found.

Changes in the second edition of CHOPCHOP.


CHOPCHOP has completely new features:

  1. CRISPR/Cpf1 mode
  2. CRISPR/Cas9 nickase mode
  3. targeting to promoter regions
  4. support for truncated sgRNAs
  5. offtarget search up to 3 missmatches
  6. self-complementarity scoring for sgRNAs
  7. support for orthologous type II CRISPR/Cas PAMs
  8. new efficiency scoring metrics based on large-scale studies
  9. scoring of complementarity of sgRNAs against backbone regions

In addition, the web interface has the following improvements:

  1. mobile friendly
  2. lots of new organisms
  3. cookies that remember your last query
  4. downloadable table with designed primers
  5. results integrated with the UCSC genome browser


CHOPCHOP has fixed the following bugs:

  1. fasta/genome input switch history
  2. fasta input scoring of off-targets
  3. fasta input bug
  4. repetitive sgRNAs
  5. shift in results view
  6. infrequent strand issue
  7. summary of off-targets at the PAM N position