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Bridger #
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Bridger #

Introduction #

New Assembler named as Bridger which combined the features from exist assemblers, i.e. Cufflinks (Reference based assembler)and trinity (denovo assembler) to overcome/improve the multiple k mer statergy which used in earlier de-novo assemblers for assemble the low and highly expressed transcripts and to get the realible Isoforms.

workflow #

Source #

Bridger is available at https://sourceforge.net/projects/rnaseqassembly/files/?source=navbar webcite.

Example Command #

Bridger.pl  --seqType fq --left Pair_R2.fq --right Pair_R1.fq --kmer_length 25 --CPU 30 --output k25 --clean
  • From my expereince its performed well in lottia transcriptome assembly, when compared to Trinity, Trans ABySS and Oases. The quantitative metircs are CEGMA and % of reference mapping.

output files #

  • path_search.commands
  • Assemble.log
  • Bridger.fasta

Notes #

At present its not able to assemble combination of (Pair and Single)

0.0.1_20140628_0