Detection of alternatives by local assembly of short reads
The alternatives source code is hosted on github:
git@github.com:gt1/alternatives.git
alternatives needs libmaus2 [https://github.com/gt1/libmaus2] . When libmaus2
is installed in
- autoreconf -i -f
- ./configure --with-libmaus2=${LIBMAUSPREFIX} \
--prefix=${HOME}/alternatives
- make install
The program expects a .hwt file produced by bwtb3m [https://github.com/gt1/bwtb3m] as input. This .hwt file can be produced using
fagzToCompact verbose=0 outputfilename=reads.compact reads.fa.gz
bwtb3m inputtype=compactstream sasamplingrate=32 isasamplingrate=32 \
outputfilename=reads.bwt numthreads=1 reads.compact
alternatives reads.hwt
The program will then construct an overlap graph and extract path alternatives in files prefixed by reads_bubbles_multi_indel_. These files are stored in the FastA format. A complete example can be found in the script example.sh in the source tree . A multiple alignment tool like mafft can be used to show indels in the assembled alternatives. The example.sh script for instance produces such a file (BRCA2mod_filtered_bubbles_multi_indel_48_0_0_0.clustal) with the following region:
0_0_0 atatggcttataaaatattaatgtgcttctgttttatactttaacaggatttggaaaaac
0_0_1 atatggcttataaaatattaatgtgcttctgttttatactttaacaggatttggaaaaac
************************************************************
0_0_0 atcagggaattcatttaaagtaaa------------------------------------
0_0_1 atcagggaattcatttaaagtaaatagctgcaaagaccacagaaaaacatcagggaattc
************************
0_0_0 ------------tagctgcaaagaccacattggaaagtcaatgccaaatgtcctagaaga
0_0_1 atttaaagtaaatagctgcaaagaccacattggaaagtcaatgccaaatgtcctagaaga
************************************************
0_0_0 tgaagtatatgaaacagttgtagatacctctgaagaagatagtttttcattatgtttttc
0_0_1 tgaagtatatgaaacagttgtagatacctctgaagaagatagtttttcattatgtttttc
************************************************************