Sequana

~~~~~~~~~~~

* BUGS:

- Fix bug in cutadapt pipeline when there is no adapters. Force a dummy
adapters (XXX) otherwise trimming is performed on read1 only

* NEWS:

- compressor rule and script available.
- coverage annotation
- multiple_summary draft

~~~~~~~~~~~

* NEWS:

- add a docker
- sequana_summary standalone
- sequana_mapping standalone
- Module has an overview field

* BUG FIXES:

- cutadapt report handles single-end tables. Fix the reverse complement
adapter files for the paired-end case

* CHANGES:

- sequana_standalone: final version with stats

~~~~~~~~~~~~~~~~~~~~~~~~

* NEWS:

- sequana_coverage standalone
- de-novo pipeline

* CHANGES:

- Remove AdapterDB, a draft version that uses Kraken to detect adapters. Not
relevant anymore
- config.yaml is now in each pipeline to have a simplified version
- sequana can known use single_indexed or multiple_indexed adapters, which
are also provided within sequana (Nextera and PCR free cases)
- Release for production (quality_taxon pipeline)

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

* NEWS:

- rule data added and used in phix_removal (fastq_sampling + raw data switch)
- kmer module
- sequana_taxonomy standalone

* CHANGES:

- reports are now in ./sequana/reporting
- MAJOR refactoring of report/ directories in all pipelines to make them
independent from the temporary analysis, which can then be removed.

* BUGS:

- Fix running median issue in bedtools (window size larger than contig size)

~~~~~~~~~~~~~~~~~~~~~~


* NEWS:

- KrakenDownlad class: download kraken_toydv from sequana/data repository or
minikraken into a local directotry
- New method in FastQC to show ACGT content
- Genomecov renamed into GenomeCov
- Update main script significantly to create multiruns and handle adapters
- GC content and plot GC vs coverage added in GenomeCov

* CHANGES:

- sequana_data by default looks into resources/testing directory
- in fastq module: FastQC a bit faster andFastQRandom class removed
- add a moving_average function in misc module

* BUGS:

- sequana_data was showing __init__ and __pycache__ as possible data sets
- databases: filelist as a list was not implemented
- in fastq.FastQ extra_head in gzip mode was missing the last row



prior 0.1.5 June 2016
~~~~~~~~~~~~~~~~~~~~~~

* NEWS

- sequana_taxonomy standalone available (kraken + krona)
- sequana standalone available
- quality_taxon pipeline available
- module coverage for theoretical computations
- add gallery in the documentation

* CHANGES:

- module vcf_to_snpeff renamed as snpeff

* BUG:

- Fix bug in running median (shift)