Skip to content

Latest commit

 

History

History
108 lines (58 loc) · 3.32 KB

CHANGELOG.md

File metadata and controls

108 lines (58 loc) · 3.32 KB
Raw

kromsatel changelog

2022-02-23 edition

Some minor modifications:

  1. Kromsatel now terminates with an error if forward-read file (-1/--reads-R1) and reverse-read file (-2/--reads-R2) are actually the same file.
  2. Kromsatel now prints its settings, which are used for a current run.

Version change: 2.0.a --> 2.0.b.

2022-01-25 edition

Major unpdate.

  1. Kromsatel now does not depend on numpy as pandas Python packages.
  2. The core kromsatel algorithm has been completely rewritten.
  3. Kromsatel now can process both unpaired and paired-end reads.
  4. "db_scripts" have been removed.

Version change: 1.6.b --> 2.0.a.

2021-12-01 edition

Kromsatel now keeps whole fastq read heders in output files instead of just the part before the first space.

Version change: 1.6.a --> 1.6.b.

Add option -o/--outdir (output directory) to kromsatel.py.

Version change: 1.5.a --> 1.6.a.

2021-05-21 edition

Improved algorithm for removing primer sequences. Although it slows kromsatel down twofold, it removes primers pretty well.

See section "Removing primer sequences" in README for details.

Version change: 1.4.a --> 1.5.a.

2021-03-29 edition

Added possibility for kromsatel to remove primers sequences from reads being processed. To do that, you should create your BLAST database using fasta file of amplicons, in which primer sequences are removed. Those files do not contain phrase _with-primers in their names (see folder amplicons-fasta/ in the repo).

Added script db-scripts/make-db.sh version 1.0.a

Version change: db-scripts/make-amplicons.sh: 1.0.a --> 1.1.a.

2021-03-05 edition

  • Improved performance ~ 2.3 times.
  • Enabled parallel read processing (-t).
  • Changed the very algorithm: it no longer looks if an alignment spans from primer to primer (or "starts" at one primer and interrupts somewhere in beteen). Now it just removes too short alignments (see options --am and --im).
  • Added options -c, --am, --im.

Version change: 1.3.b --> 1.4.a.

2021-01-27 afternoon edition

Made the algorithm less brutal to those reads which do not span from primer to primer. Now kromsatel allows offset of 10 bp from both ends (this offset is no longer actual).

Version change: 1.3.a --> 1.3.b.

2021-01-27 edition

Added script make-amplicons.sh and new (alternative) set of amplicons: amplicons-db/nCoV-2019-alt_amplicons.fasta.

Primers for this new amplicons are from here.

2021-01-24

Moved kromsatel from cager-misc to this separate repo.

2021-01-06 edition

  • kromsatel: fixed bug that would cause kromsatel to prefer minor amplicons over major ones.

Version changes:

  • kromsatel: 1.2.e -> 1.3.a

2020-12-02 edition

  • kromsatel: output files naming changed: now "cleaned" is suffix, not prefix.

Version changes:

  • kromsatel: 1.2.d -> 1.2.e

2020-11-14 edition

  • kromsatel now works 2 times faster.

Version changes:

  • kromsatel: 1.2.c -> 1.2.d

2020-11-13 edition

  • kromsatel: performance improved.

Version changes:

  • kromsatel: 1.2.b -> 1.2.c

2020-11-12 edition

  • kromsatel version 1.2.a added, then added version 1.2.b with code commented and some optimized operations.