Magic-BLAST 1.4.0: August 10, 2018

New features
  • New option: -no_discordant to report only concordant read pairs
  • Report strand-specific alignments with -fr and -rf flags for forward-reveresed and reversed-forward
  • New option to control repeat filtering: -max_db_word_count. 16-base words that appear in the genome more than this number of times will be filtered (default is 60).
Improvements
  • Improved sensitivity: count for frequent database words to be filtered was increased to 60 (used to be 10). This threshold can be changed with the -max_db_word_count option.
  • Non-cannonical splice signal now require longer alignments on the exon, with score at least 50 on both sides of an intron.
  • More informative error messages for SRA access
  • Much better handling of non-cannonical splice sites and compositionally biased genomes
Bug fixes
  • Alignments no longer stop prematurely
  • Fix for not returning unmapped reads when none is aligned
  • Magic-BLAST no longer reports zero-length introns
  • Parameters of the score threshold as a function of read length are no longer 100 smaller than specified by the user

Magic-BLAST 1.3.0: September 15, 2017

New features
  • The alignment cutoff score (-score option) can be expressed as either a constant or a function of read length in this format: L,b,a for a * length + b
  • Maximum edit distance cutoff for alignments can be specified with -max_edit_dist option
  • SRA caching is now turned off by default and can be turned on with the -sra_cache flag. When accessing sequences in NCBI SRA repository the data can be cached in a local file so that it is not downloaded over the network again when reused later. It may result in very large local files and is only needed if you use SRA accessions multiple times, have very limited network bandwidth and a large disk space.
Improvements
  • Unmapped reads are reported in the SAM and Tabular reports, use -no_unaligned option to not have unaligned reads reported
  • The XS tag (used by transcript assemblers) is now reported in SAM output
  • The score threshold (-score option) now applies to the whole spliced alignment
  • The query batch size (number of reads processed at a time) is now controlled with environment variable BATCH_SIZE expressed in cumulative number of bases
  • The default mismatch and gap extension penalties are now set to 4
  • Improved sensitivity and run time
Bug fixes
  • Read ids for pairs are printed properly in the SAM format (no “.1” “.2” or “/1” “/2”)
  • The secondary alignment bit (256) is set in SAM flags
  • Maximum intron length option -max_intron_length works properly

Magic-BLAST 1.2.0: February 17, 2017

Improvements
  • Improved multi-threading for larger genomes
  • Improved splice site detection
Bug fixes
  • Magic-BLAST now works with multiple SRA accessions
  • Fixed the macOS dmg installer that used to remove BLAST+ binaries
  • The -seqidlist option is no longer ignored

Magic-BLAST 1.1.0: November 4, 2016

Improvements
  • -sra option connects to NCBI via HTTPS
  • Results are formatted with ‘bare’ accessions
  • Tabular output includes a header with column titles
Bug fixes:
  • Fixed SAM flag values

Magic-BLAST 1.0.0: August 19, 2016

  • First release