Bug fix

Fix metadata default for is_single_end function.

aTRAM improvements

• You can optionally shuffle input sequences in atram_preprocessor.py
• Added more assembler options for Abyss.
• Update assembler flags to match the arguments of the assemblers themselves
• Fix errors related to assemblers timing out.
• Various minor bug fixes.

Atram improvements

• Atram can now be installed via conda. thanks to Ulises-Rosas
• There is now a framer utility for preparing assemblies for phylogenetic analysis
• There are numerous bug fixes and other minor improvements

aTRAM Stitcher

We have added a "stitcher" utility to aTRAM.

Minor bug fixes

v2.1.2

Fix double ">>" for fasta output #244

Fixes and improvements

• Fixed bug affecting the --query-split option
• Allow gziped and bziped files as input to atram_preprocessor.py

Improve aTRAM stability

There were many minor improvements and bug fixes but the highlights of this release are:

1. Improve the stability of SQLite when processing large files on fast machines. This issue was manifesting itself as an "sqlite3.OperationalError: database is locked" error.
2. We changes how temporary files are handled. Most temporary files are now deleted between each aTRAM iteration. This reduces the disk footprint of aTRAM and helps with larger assemblies.
3. aTRAM now displays the number of blast hits at each iteration. This gives you more information about how well aTRAM is progressing or why an assembly may fail.
4. We added the new blast option --word-size. If entered, this is passed to directly to blast.

Release 2.0

Release 2.0

Improve instructions, report formats, and fasta file handling

We have gathered numerous small changes to the instructions, aTRAM report output files, and fasta file handling into a release.

We also reduced the number of required modules in requirements.txt and separated the testing requirements into its own requirements_test.txt file.

Pipeline fixes

Now catching more errors the assemblers throw at atram. It will also continue with the pipeline's other assemblies after one assembly breaks.