Hello,
A new version of FASTX-Toolkit is available for download at http://cancan.cshl.edu/labmembers/gordon/fastx_toolkit/index.html
Improvements include:
* fastx_collapser can now re-collapse an already-collapsed FASTA file. you can collapse+trim+collapse without losing counts or getting error messages.
* new tool: fastx_uncollapser uncollapses a FASTA file (reverse the effect of fastx_collapser). This tool can also uncollapse a tabular file with collapsed sequence-identifiers. In galaxy these are split into two separate tools: http://cancan.cshl.edu/labmembers/gordon/fastx_toolkit/galaxy.html#fasta_unc... http://cancan.cshl.edu/labmembers/gordon/fastx_toolkit/galaxy.html#seqid_unc... On the command line, it's the same program.
* new tool: fastq quality trimmer trims a FASTQ file based on quality score cut-off. http://cancan.cshl.edu/labmembers/gordon/fastx_toolkit/galaxy.html#fastq_qua... (tool suggested by Matthew Baranski).
* fastx_trimmer can now trim N bases from the end of the sequence (instead of having to specify absolute length). In Galaxy, this is a separate tool: http://cancan.cshl.edu/labmembers/gordon/fastx_toolkit/galaxy.html#fastx_tri... On the command line, it's the same program. (option suggested by Matthew Baranski).
* fastx_quality_stats supports new format with statistics per-nucleotide. (so you can find avg/min/max/med quality of each nucleotide in each cycle).
* Fixed several compilation errors and warnings on different platforms.
Comments are welcomed, -gordon.