Tham Cheng Yong posted a comment on discussion General Discussion

Hi, may I know what is the default read coverage cut-off parameter for SV calling? And if I am able to adjust it? Thanks Tham

Ken posted a comment on discussion General Discussion

Hi Sitan, When calculating breakpoints supporting reads, we allow a [-1, +1] shift around the junction to alleviate alignment ambiguity. This may overestimate the split reads around breakpoints. But estimation of SV frequency based on split reads may underestimate it as well. To be comparable, I suggest you use (column 19 + column 29)/(column 16 + column 26). Col 19 and Col 29 are high-quality split read numbers. These fields (column 11 to column 39) are: cluster_id, contig_id, contig_size, reads_used_for_assembly,...

novoBreak released /README.md

Ken posted a comment on discussion General Discussion

Can be found at https://github.com/czc/nb_distribution

lee duhee posted a comment on discussion General Discussion

Hello Zechen. I was trying to run novoBreak. but there were some error. I using AWS because i dont have high-perfomance computer. NovoBreak is in /home/ec2-user/novoBreak_distribution_v1.1.3. And i export the PATH too, but it didnt work well. export $PATH -bash: export: `/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/opt/aws/bin:/home/ec2-user/.local/bin:/home/ec2-user/bin:/home/ec2-user/novoBreak_distribution_v1.1.3': not a valid identifier And i run by command 'sh run_novoBreak.sh...

Ken posted a comment on discussion General Discussion

you should export the path to the novoBreak_distribution directory. The command should be "export PATH=$PATH:/data/tmp/huebnerj/novoBreak_distribution_v1.1.3rc".

Ken posted a comment on discussion General Discussion

If there is no normal control, a simulated normal bam file (no coverage need) can be used to meet the interfaces of novoBreak. But the results would be both somatic and germline events. You can use wgsim to simulate raw reads from reference and align them using bwa to generate a bam file as "normal".

Ken posted a comment on discussion General Discussion

The source code of novoBreak is on the SourceForge already. Simply use "git clone https://git.code.sf.net/p/novobreak/git novobreak-git && cd novobreak-git && make" and copy the binary of novoBreak to replace the "novoBreak" in novoBreak_distribution_v1.1.3rc should be fine. If the software in the novoBreak_distribution_v1.1.3rc directory cannot use due to Linux environment (such as samtools), simply download the source and compile, install and copy to the novoBreak_distribution_v1.1.3rc directory...

christos proukakis posted a comment on discussion General Discussion

so I am also unable to run this on our main server Linux any help will be very welcome! bash novoBreak_distribution_v1.1.3rc/run_novoBreak.sh novoBreak_distribution_v1.1.3rc/novoBreak hg19.fasta bamfiles/P38_14.MB2.sorted.dup_removed.q40.bam bamfiles/P38_14CER.sorted.dup_removed.q40.bam 2 -PWD readlink: invalid option -- 'P' Try 'readlink --help' for more information. mkdir: missing operand Try 'mkdir --help' for more information. novoBreak_distribution_v1.1.3rc/run_novoBreak.sh: line 26: /home/rmgtcpr/novoBreak_distribution_v1.1.3rc/novoBreak/novoBreak:...

christos proukakis posted a comment on discussion General Discussion

So i see that readlink is a problem, and i did brew install coreutils so i can use greadlink, and I edited the file changing readlink to greadlink everywhere i also did brew install perl in case that was the problems now I get someting to do with symlinks which someone commented on, probably beyond me to solve... greadlink: invalid option -- 'P' Try 'greadlink --help' for more information. usage: mkdir [-pv] [-m mode] directory ... /Volumes/SD/novoBreak_distribution_v1.1.3rc/run_novoBreak.sh: line...

christos proukakis posted a comment on discussion General Discussion

Hello I would really like to use this, but 1) I am trying on a single core i7 mac with 16 G of RAM. Is there any chance it will work, even it takes days, or should I give up? 2) it doesnt wan to start- am i doing this the right way? bash /Volumes/SD/novoBreak_distribution_v1.1.3rc/run_novoBreak.sh /SD/novoBreak_distribution_v1.1.3rc /Volumes/SD/bwa0712/hg19.fasta /Volumes/SD/MPS_work/P38_14.MB2.sorted.dup_removed.q40.bam /Volumes/Toshiba4Tb/WGSdata/mayo_MPS/P38_14.MB2.sorted.dup_removed.q40.chr4.sorted.bam...

Nick Riddiford modified a comment on discussion General Discussion

Hi Zechen, I'm attempting to use your tool novoBreak by running 'run_novoBreak.sh',...

Nick Riddiford posted a comment on discussion General Discussion

Hi Zechen, I'm attempting to use your tool novoBreak by running 'run_novoBreak.sh',...

Ken posted a comment on discussion General Discussion

Hi Wenkai, You may try the inherent second filter filter_sv2.pl. Or a tip you may...

Giuseppe Narzisi posted a comment on discussion General Discussion

In the Nature Methods paper novoBreak is used to call indels on the DREAM datasets....

Yunku Yeu posted a comment on discussion General Discussion

Hi, I'd like to report and share some information which is not described in README...

novoBreak released /novoBreak_distribution_v1.1.3rc.tar.gz

novoBreak released /novoBreak_distribution_v1.1.3.tar.gz

novoBreak released /novoBreak_distribution_v1.1.1.tar.gz

Zechen Chong committed [acdc80]

new file: asm_R2.c

Chong committed [6a2a6a]

usage update

Zechen Chong committed [1fab90]

On branch testbitvec

Zechen Chong committed [3ce096]

On branch feature-bam

Zechen Chong committed [6acf4f]

On branch feature-bam

Zechen Chong committed [9678c5]

change samtools to v.0.1.19

Zechen Chong committed [d3d1e2]

print out read pair ids

Zechen Chong committed [ce1056]

fixed a bug when encap bitvec

Zechen Chong committed [e3edef]

fixed a read length < kmer size bug

Zechen Chong committed [7d9724]

v1.05

Zechen Chong committed [a7e464]

On branch local_assembly

Zechen Chong committed [c7a1bb]

On branch loadid

Zechen Chong committed [0da1f2]

fixed bitvec init size type bug

Zechen Chong committed [706729]

On branch feature-bam

Zechen Chong committed [cf8614]

On branch feature-bam

Zechen Chong committed [5e1606]

On branch testbitvec

Zechen Chong committed [3910b4]

modified: filter_kmer.c

Zechen Chong committed [e8e0d7]

report somatic and germline kmer reads now

Zechen Chong committed [d81d8b]

modified: Makefile

Zechen Chong committed [2c52b3]

On branch filterkmer

Zechen Chong committed [8ba26b]

hash reference first then process reads

Zechen Chong committed [323c21]

On branch feature-bam

Zechen Chong committed [370508]

On branch feature-bam

Zechen Chong committed [27de30]

fixed a bam header bug

Zechen Chong committed [6930a5]

Initial commit

Zechen Chong committed [8cf465]

modified: Makefile

Zechen Chong committed [4df07e]

On branch filterkmer

Zechen Chong committed [982778]

using bitvec to represent kmers in reads

Chong committed [0cc6d3]

fixed warnings of selfassignment and one error ...

Zechen Chong committed [cf47c5]

modified: filter_kmer.c

Zechen Chong committed [837af2]

fixed a bug of freeing chash values

Zechen Chong committed [ccd2ce]

modified: file_reader.c

Zechen Chong committed [ece2f9]

sequences are loaded, then only id loaded

Zechen Chong committed [e3735c]

added new files

Zechen Chong committed [238ade]

nothing to do

novoBreak released /novoBreak_distribution_v1.1.tar.gz

novoBreak released /novoBreak.tar.bz2

novoBreak released /README