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The `cov-cutoff` parameter remains a mystery to the Spades user community. It used to be `auto` and now it is `off`.
Would it be possible to add an explaination to the document explaining it?
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Hi,
I'm trying to build a Docker container with **mlst**, but it seems not working properly.
I'm using Blast+ v2.6.0 binaries and **mlst** GitHub release v2.9 (`wget https://github.com/tseemann/ml…
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I can't get the bwa step to proceed. When it starts running the bwa mem command it returns an error ('Error running command, check snps.log'). It happens when I use fasta or gbk (prokka 1.12 output) a…
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Actualy we use the last extension in filename to choose the compression format, we can replace it by read the magic number.
- gz : 1f 8b (2 bytes)
- bz2 : 'BZ' (16 bytes)
- xz : { 0xFD, '7', 'z',…
natir updated
7 years ago
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Hi, I was just wondering if there's a multiple threading option for DBG2OLC - cause it seems to be quite slow and takes only 5% cpu on a multicore server ....
What am I missing?
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FASTQ files could be compressed in BFQ format (see [fastqutils](http://ngsutils.org/modules/fastqutils/bfq/) for more information). In picard, there is a [BamToBfqWriter](https://github.com/broadinsti…
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Tim and Nils;
Thanks for all the recent work supporting duplex reads. I've been working on adding support for this into bcbio and updated to the latest development version to get the duplex fixes in …
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BDS running with SGE doesn't seem to see some jobs finish. This doesn't happen all the time. Here's an example. I have 27 samples consisting of 2 files each (fq1, fq2). For each sample, I start a …
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By default, the FASTQ format is gzipped and `-dgz` option allows to disable. This option should disappear in favor of one enum which allows to use a different kind of compression with FASTQ format (bg…
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Hi Brad,
Just a quick question. I noticed that when we start a new run, the compressed fastq files we use as input are decompressed and then recompressed in bgzip format. This takes about 20 min pe…