IgBLAST 1.9.0 release includes AIRR rearrangement reporting


IgBLAST 1.9.0 supports the adaptive immune receptor repertoire (AIRR) standard for sequence analysis results. The AIRR format is available on web IgBLAST as well as in the standalone IgBLAST tool, with the -outfmt 19 option.

Supporting this new schema in IgBLAST will enhance the increasing amount of repertoire studies that use next-generation sequencing technology to generate very large sets of Ig/T-cell receptor rearrangement analysis data.

IgBLAST facilitates the analysis of immunoglobulin and T cell receptor variable domain sequences. Get IgBLAST on FTP. A new manual is on GitHub.

IgBLAST 1.8.0 release


A new version of IgBLAST is now available on FTP, along with a new manual on GitHub. This release has the following improvements:

  1. The igblastn executable can now multi-thread much more efficiently for large sets of queries. The default number of threads is now four, but can be changed with the -num_threads option.
  2. The igblastn executable can now take an SRA accession as the query input. The search runs on the local machine, but the queries are retrieved from the SRA repository at the NCBI. Use the -sra rather than the -query option to enable.
  3. A lower default nucleotide mismatch penalty values for finding D and J genes (from -4 to -2 and from -3 to -2, respectively). This improves accuracy in finding the best D and J gene hits for moderately mutated sequences.

Our web IgBLAST page also uses the new default nucleotide mismatch penalty values (i.e., -2 for finding both D and J genes).

IgBLAST facilitates the analysis of immunoglobulin and T cell receptor variable domain sequences.

New releases from NCBI: IgBLAST 1.7.0 and Sequence Viewer 3.21


IgBLAST 1.7.0 release

A new version of IgBLAST is now available on FTP, with the following new features:

  1. Specify whether overlapping nucleotides at VDJ junctions are allowed in matching V, D, and J genes.
  2. Set a custom J gene mismatch penalty
  3. Report the CDR3 start and stop positions in the sub-region table
  4. Use alignment length instead of percent identity as the tie-breaker for hits with identical blast scores, improving accuracy in the V, D, J gene assignment.

IgBLAST was developed at the NCBI to facilitate the analysis of immunoglobulin and T cell receptor variable domain sequences.

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