BBMap Activity
BBMap short read aligner, and other bioinformatic tools.
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Activity for BBMap
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BBMap released /BBMap_39.60.tar.gz
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Martin Mokrejs created ticket #78
filterbysequence.sh does not accept padding dashes
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darked90 created ticket #77
demuxbyname.sh Exception in thread "main" java.lang.AssertionError: 22, 23, '^@'=0
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Brian Bushnell posted a comment on ticket #74
I still spend all of my time developing BBTools. However, due to internal politics, the JGI website has changed to not feature any JGI-developed bioinformatics software (BBTools, MetaHipmer, etc). Feel free to send an email to JGI's director (nmouncey@lbl.gov) if you think it is helpful for JGI's users to have bioinformatics software such as BBTools on its website, because helping users is supposed to be our goal.
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William Nicholson modified a comment on ticket #74
Okay, the above URL linked from the project website still does not work. However, I have found what appears to be the original content at https://archive.jgi.doe.gov/data-and-tools/software-tools/bbtools/ . I'm not sure the implication of this now being on the "archive" website - does that mean the project has been wound up? Although that doesn't appear to be consistent with the amount of recent updates (since the above post) to BBMap/ BBTools, William
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Okay, the above URL linked from the project website still does not work. However, I have found what appears to be the original content at https://archive.jgi.doe.gov/data-and-tools/software-tools/bbtools/ . I'm not sure the implication of this now being on the "archive" website - does that mean the project has been wound up? William
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Assa Yeroslaviz posted a comment on ticket #76
I'm asking because I can see very different results in the read number of duplicated reads when checking a specific file. When running it with fatqc I get over 90% duplications, when using fastp to calculate duplications I have only 47.3% duplicated reads, but when testing it with clumpify I get 0.213% duplication rate. I can't explain these differences, unless I'm using the wrong parameters for searching duplications. The commands for the two tools are as followed: fastp --in1 ${prefix}${file}_R1.fastq.gz...
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dupedist value for AVITI machine
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Heyu Lin posted a comment on ticket #75
Great. Thank you Brian!
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Found the problem in the parser; it will be fixed in 39.20.
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OK! I'll look into it and get back to you.
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hi Brian, thanks for the reply. It's the newest version - 39.19. I just deployed it by conda yesterday.
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That's odd; looks to me like it should be working. What version are you using?
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Parameter 'stats2' in rqcfilter2.sh is not recognized
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Samantha M Zarnick posted a comment on discussion General Discussion
Does filterbyname remove all reads in the fastq files that match a read name in the txt file? Are duplicates in the input files an issue?
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Project website for BBMap appears to have disappeared
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Ryan Zhu created ticket #73
repair.sh swaps sequences in the output fastqs
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Jared Brewer created ticket #72
java.lang.AssertionError with forcemerge=t
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39.15 is out now.
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reformat.sh producing output with 4 reads having the same id
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Hmmm... looks like the issue here is that the intermediate fastq file is not really interleaved. Sam/bam files are not interleaved in the first place and should never be treated as such; the order of records is arbitrary and reformatting them as fastq (with samtools) doesn't change that. If you force Reformat to process a noninterleaved file as interleaved, strange things will happen; in this case, the records for that pair are nonadjacent and that causes the header replication, as per the sam specification...
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Jordi Camps posted a comment on ticket #71
:-O Blazing fast! Thanks a lot! We will run this typically with pair end data. Let's see how it goes. The flag to classify reads as duplicates only if UMIs match will be useful too. There are a lot of ways to decide if two different UMIs are the same, but this basic method (exact identity) will be more than enough for a quick classification of non-aligned data.
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Issues when reading IDs with UMIs
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All fixed; will be released in BBTools 39.15. Along with the new flags "umi" and "umisubs" so that you can require reads to only be classified as duplicates if their UMIs match.
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Thanks for this report... JGI doesn't use UMI's so I haven't seen them before in Illumina reads. I've duplicated the error and am modifying my header parsers to support UMIs, so that will work correctly in the next release.
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Issues when reading IDs with UMIs
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Brad Langhorst created ticket #70
reformat.sh producing output with 4 reads having the same id
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Eric Boyden posted a comment on discussion General Discussion
I was looking for a java-based alternative to either cutadapt or ngmerge, and bbmerge seems to be able to do much of what both other tools can do (primarily I was looking for fixed read trimming, quality trimming, and paired read dovetail trimming). A few suggested improvements: * Allow simultaneous fixed trimming and q-trimming. Right now it seems like q-trimming supercedes fixed trimming if both are specified, regardless of which end you want to trim in each case; but there are situations where...
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I was looking for a java-based global short-read aligner and this software performs excellently, with lots of neat features that many other aligners lack. In descending order of priority, here are some ideas for improvement: * Update SAM spec to v1.6 (currently 1.3/1.4), primarily to produce an updated @HD line to indicate query grouped output (GO:query). Many downstream tools (e.g. some fgbio tools) rely on this and won't work unless this is explicitly specified, and resorting just to add this annotation...
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When I wrote that, PacBio did not have paired reads. They have a new sequencing machine now for short reads that I think does produce pairs but I have not seen any data for it so I'm not sure of the header structure.
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Max Rozenblum posted a comment on ticket #69
I will check in with the lab, but my understanding is that these came from a NextSeq or NovaSeq and didn't have any modifications. Thanks for the quick response. I took a peak at FASTQ.java and saw the following code block: // Here we try to weed out PacBio, which will differ after the last slash: for (int i = idxSlash1 + 2; i < len1; i++) { if (id1.charAt(i) != id2.charAt(i)) { return false; } } I am using reformat.sh to do the following: - make sure reads are paired - count the number of reads/bases...
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