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KDBio
Tool for Alignment of Pyrosequencing Reads

Latest Development Version (Beta)

P-TAPyR v1.3-beta4 (19-07-2013)

· This is a preview version of the upcoming v1.3 with multi-threading support
· Please read the included README.TXT for usage information
· It features a new index structure, so you need to re-index the references
· This is a beta version and thus it may still contain some bugs
· Full changelog coming soon

Source Code (Stable)

tapyr v1.2c

Install

tar -xzvf tapyr.tar.gz
make

Developments in progress

  • (v1.3) Output alignment consensus in ACE and mpileup and SNPs in VCF
  • (v1.3) Faster and more memory efficient BWT-index building algorithm
  • (v1.3) Support for reference sequences with size up to 4Gbps (e.g. Human genome)
  • (v1.3) Support for N's in the reference sequence

History

(29-01-2012) v1.2c:

· Support for Ion Torrent's mate-pair SFF files
· Added auto-detection of Ion Torrent SFF files
· Added auto-detection of 454's GS Junior and FLX+ from SFF file
· Added detection of inexact paired-end linker sequences
· Added tool to generate consensus sequence (command: C)
· Added positions markers to mapping plot images
· Fixed broken detection of paired-end linker sequence
· Fixed bug in SAM processing code for 'S' CIGAR operation
· Fixed bug causing negative mapping quality values
· Fixed bug in arguments parsing code

(02-11-2011) v1.2b:

· Support for multiple input read files simultaneously
· Support for 454's paired-end SFF files
· Added auto-detection of source 454 instrument from SFF file
· Added tool to split paired-end SFF files into both mates (command: P)
· Added tool to convert SAM file to TSV file (command: T)
· Changed default read identity percentage to 80%
· Changed default reporting strategy to all hits

(10-10-2011) v1.2a:

· Fixed wrong read position when using thorough mapping mode in some cases
· Improved support for multiple references
· Changed DP algorithm to report indels always on the same side of homopolymers
· Changed SAM output to report only the best scoring hit for each read
· Changed SFF conversion tool output from FASTA to FASTQ format
· Changed FASTQ conversion tool to support multiple line sequences
· Changed MIN/MAX paired-end read options to avg distance and std deviation
· Added progress bar for read mapping operation
· Added option to output all hits instead of only the best one
· Added option to save unmapped reads
· Small speed improvements

(22-09-2011) v1.2:

· Support for paired-end reads
· Support for multiple reference sequences inside the same file
· Added local read mapping plot (command: V startPos endPos)
· Added read mapping qualities to SAM output
· Removed pre-processing of reads file at startup
· Fixed off-by-one position error when a mismatch occurred in 1st char of read
· Fixed bug in DP phase that reported more errors than true in end segments
· Changed output file name suffix from "*-output.sam" to just "*.sam"
· Some speed improvements
· Other small changes

(25-07-2011) v1.1:

· Support for direct loading of FASTQ and SFF files
· Added visualization option for global alignment map (command: V)
· Fixed bug that was causing slowdowns in the DP phase
· Other minor changes

(07-03-2011) v0.9a:

Some bug fixes

(16-12-2010) v0.9:

First public release