barcodeasm's Introduction

BarcodeAsm - local read cloud assembler

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 longranger pipeline
-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 window
hits.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

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