Kneaddata

* By default alignments for paired input files now include discordant alignments. To restrict these alignments and only allow concordant alignments (which was the default in prior versions) add the option "--no-discordant".
* A new option "--cat-pairs" allows for alignments of paired end reads as single end (ignoring pair identifiers). This differs from the default alignment mode as the default mode will first align as pairs and then as single end if no concordant alignments are identified.
* A new option "--reorder" which can be used with discordant alignments will reorder the clean fastq files to the same order as the original input files.
* If new illumina sequence identifiers are found, they are replaced with identifiers similar to the original format to maintain pair identification with alignments.
* A mouse bowtie2 database is now available for download.

New Features

* A human metatranscriptome bowtie2 database is now available for download.
* A ribosomal RNA bowtie2 database is now available for download.
* A new option "--cat-final-output" will create a single output file from all final output files for paired-end inputs.
* A new script kneaddata_read_count_table will create a table of read counts (raw, trimmed, decontaminated, final) for all logs provided.

Bug Fixes

* If the output prefix selected is the same as the basename of the input file and the input file is gzipped, the final output file for single-end reads would be deleted as the name was the same as the temp gunzipped input file. A temp file is now used to store the gunzipped input file to prevent overlap.

New Features

* KneadData is now python3 compatible.

New Features

* New options were added to run fastqc at the beginning and/or end of the workflow. Please note these options require fastqc be installed.
* Input files can now be gzipped. They can also be of the SAM or BAM format. Please note with BAM input files SAMTools must be installed.
* The default Trimmomatic options now have the minimum length set to 70% of the length of the reads in the input file.

New Features

* Bypass and run options have been added so a workflow can include any number of tools. There are nine possible combinations to run Trimmomatic, Bowtie2/BMTagger, and TRF.
* Functional and unit tests were added. To run use $ kneaddata_test. Please note this requires external dependencies be installed like Bowtie2.