This program uses fermi-lite and bead barcode information from the 10X
sequencing protocol to create local assemblies of target regions. We attempt to
identify unmapped/mismapped reads that are relevant to the local region by
enumerating the barcodes of the locally mapped reads.
To compile BarcodeAsm use the following:
git clone --recursive https://github.com/cgroza/BarcodeAsm.git
cd BarcodeAsm
./autogen.sh
./configure
make
make install
The executable should be in bin.
To run BarcodeAsm, the following arguments are needed:
- -b : path to the indexed BAM file produced by the
longrangerpipeline - -B : path the barcode sorted and indexed BAM file from above
- -r : path to BED file containing the start and end of local assembly windows
- -F : path to FASTA file listing sequences of interest to be checked in the newly assembled contigs (optional)
- -g : path to the genome FASTA file
- -G : output GFA for each assembly window
- -o : minimum required read overlap during assembly
fermi-lite - -P : pop small bubbles in heterozygous regions (optional). Keeps the larger bubbles.
- -S : separate reads by phase before assembly (optional)
- -o : minimum overlap between reads (default 30)
- -a : import all reads belonging to the barcodes in the local assembly window (optional)
- -t : number of threads (default is 1, needs 2GB memory per thread)
The outputs are:
contigs.fa: FASTA file containing all assembled contigs. Names describe the local assembly window and the phase (p1/2 is first/second phase and p0 is unphased)alignments.tsv: file describing the alignment of assembled contigs to the local windowhits.tsv: TE library (provided by -F) alignment hits against the assembled contigs for each window- local_window.gfa : GFA file for each local window that contains the assembly graph