abra
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mozack
Assembly Based ReAligner
Hi, I would like to ask about ABRA realignment of single-fragment (non-paired) reads around regions where there is a poly-A or poly-T or low complexity region where bowtie2/bwamem are unable...
I am running Abra-0.96 using abra-0.96-SNAPSHOT-jar-with-dependencies.jar It runs over 24 hours and gives me the following error: Clock time in Align and clean contigs: 49461 Sat Dec 19 21:10:43 CST...
150x whole exome (64 Mb) not completed after 24 hours w 18 cores while building all_contigs.fasta (which continues to increase in size). This is a reproducible sample specific issue as...
Hi Lisle, I found a little bug in your BED file parsing: Header lines without tab are treated as data lines. Thus, they lead to a crash because the second...
Hello, I was able to run abra for a number of BAM files. But a few of them are giving me this error: -- Fri Nov 13 03:44:57 CST 2015...
Is there a way to perform realignment without the use of a BED file, for example, in WGS cases? Thank you.
Very cool project! Does the code currently (a) try and salvage unaligned reads and (b) distant reads with potential alternate alignments. This would help for the events I'm looking for....
Producing this error with our own bams using v0.79 built on Mountain Lion. However, using the demo bam and bed file included with abra runs perfectly. Command: java -Xmx16G -jar...