IMP issueshttps://git-r3lab.uni.lu/IMP/IMP/-/issues2018-10-10T12:18:37+02:00https://git-r3lab.uni.lu/IMP/IMP/-/issues/136Accelerating the rRNA filtering step2018-10-10T12:18:37+02:00Cedric LacznyAccelerating the rRNA filtering step`sortmerna` appears to be a relatively slow program for the metatranscriptomic files we are typically processing.
An acceleration of this step would be nice!
There do not seem to be too many alternatives out there though: https://omicto...`sortmerna` appears to be a relatively slow program for the metatranscriptomic files we are typically processing.
An acceleration of this step would be nice!
There do not seem to be too many alternatives out there though: https://omictools.com/rrna-filtering-category
Some of them are web-based, hence do not really represent an alternative.
Maybe `rrnafilter` would be one, but from superficially scanning over it, it seems to be based on k-mer abundances.
While this enables the identification of candidate rRNA reads without the need for reference sequences, it could also lead to false positives, i.e., non-rRNA gene-derived sequences of high (or divergent) abundance) that are wrongly classified as rRNA gene-derived.
Not sure how the tool was tested in the original publication.
A dedicated test might be required, though.https://git-r3lab.uni.lu/IMP/IMP/-/issues/135Read preprocessing using fastp2018-10-08T16:32:54+02:00Cedric LacznyRead preprocessing using fastpMaybe [fastp](https://github.com/OpenGene/fastp) could be integrated as a preprocessing step.
According to its documentation is is (supposedly)
>like FASTQC but faster and more informative
and it integrates trimming etc. while automati...Maybe [fastp](https://github.com/OpenGene/fastp) could be integrated as a preprocessing step.
According to its documentation is is (supposedly)
>like FASTQC but faster and more informative
and it integrates trimming etc. while automatically detecting the adapters as well as
>trim polyG in 3' ends, which is commonly seen in NovaSeq/NextSeq datahttps://git-r3lab.uni.lu/IMP/IMP/-/issues/118Automate for samples with multiple runs in sequencing2017-10-03T17:04:56+02:00Shaman NarayanasamyAutomate for samples with multiple runs in sequencingSome samples are run on separate sequencing runs. Usually, users would want to pool such samples and perform analysis as if it were a single sample.
-Shaman-Some samples are run on separate sequencing runs. Usually, users would want to pool such samples and perform analysis as if it were a single sample.
-Shaman-https://git-r3lab.uni.lu/IMP/IMP/-/issues/105megahit iterations: 99-25=74 modulo 4 is 2 and not 02017-10-04T12:29:15+02:00Patrick Maymegahit iterations: 99-25=74 modulo 4 is 2 and not 0you are producing with megahit kmer assemblies from 25 to 97 with increment 4 and additional the 99 kmer assembly, which is an artefact by the megahit tool.
At some point you should change this, also in the documentation, it is misleadin...you are producing with megahit kmer assemblies from 25 to 97 with increment 4 and additional the 99 kmer assembly, which is an artefact by the megahit tool.
At some point you should change this, also in the documentation, it is misleading because 99-25=74 modulo 4 is 2 and not 0https://git-r3lab.uni.lu/IMP/IMP/-/issues/103Retain kmer graphs after assembly2017-07-06T14:24:39+02:00Shaman NarayanasamyRetain kmer graphs after assemblyThese could be potentially useful for integrated proteomic analyses.These could be potentially useful for integrated proteomic analyses.https://git-r3lab.uni.lu/IMP/IMP/-/issues/102Incorporate MultiQC2017-06-12T16:33:33+02:00Shaman NarayanasamyIncorporate MultiQCNice solution for reporting purposes:
http://multiqc.info/Nice solution for reporting purposes:
http://multiqc.info/https://git-r3lab.uni.lu/IMP/IMP/-/issues/101Automatic creation of databases after analyses2017-05-31T11:36:45+02:00Shaman NarayanasamyAutomatic creation of databases after analysesAt present, we just save text files. Possible solutions:
- MongoDB
- MySQLAt present, we just save text files. Possible solutions:
- MongoDB
- MySQLhttps://git-r3lab.uni.lu/IMP/IMP/-/issues/100Multi sample analysis2017-05-31T11:32:49+02:00Shaman NarayanasamyMulti sample analysisWe would need:
1. A means of providing multiple paired end sequences using:
- direct input to the command line
- a list of samples with their relevant paths (for very large studies)
2. After sample-wise analyses, "representative ...We would need:
1. A means of providing multiple paired end sequences using:
- direct input to the command line
- a list of samples with their relevant paths (for very large studies)
2. After sample-wise analyses, "representative genomes" can be selected using dRep (http://biorxiv.org/content/early/2017/02/13/108142)
3. Reads from each sample should be remapped to the "representative genomes" generated by dRep
4. Other possible enhancements in this regard:
- Choice for a combined assembly (i.e. pooing reads from multiple samples). This strategy might work well for smaller number of samples, technical replicates, analytical replicates and/or highly similar sampleshttps://git-r3lab.uni.lu/IMP/IMP/-/issues/99Metaproteomic analysis2017-05-31T11:26:41+02:00Shaman NarayanasamyMetaproteomic analysisMany methods available, but best candidate so far:
dx.doi.org/10.1371/journal.pcbi.1005224Many methods available, but best candidate so far:
dx.doi.org/10.1371/journal.pcbi.1005224https://git-r3lab.uni.lu/IMP/IMP/-/issues/98Digital normalization2017-05-31T11:24:59+02:00Shaman NarayanasamyDigital normalizationPotential tools that could be applied are:
- https://arxiv.org/abs/1203.4802
- http://biorxiv.org/content/early/2017/05/03/133579Potential tools that could be applied are:
- https://arxiv.org/abs/1203.4802
- http://biorxiv.org/content/early/2017/05/03/133579https://git-r3lab.uni.lu/IMP/IMP/-/issues/97predict rRNAs2017-05-31T11:34:06+02:00Anna Buschartpredict rRNAsI would love to have some rRNAs predicted within IMPI would love to have some rRNAs predicted within IMPhttps://git-r3lab.uni.lu/IMP/IMP/-/issues/96save space, compress reads2017-05-31T11:35:21+02:00Anna Buschartsave space, compress readscould IMP please automatically compress the read files from the different steps?could IMP please automatically compress the read files from the different steps?https://git-r3lab.uni.lu/IMP/IMP/-/issues/80Add new binning tools2017-11-10T03:44:08+01:00Shaman NarayanasamyAdd new binning toolsMetaBAT
binnyMetaBAT
binnyShaman NarayanasamyShaman Narayanasamyhttps://git-r3lab.uni.lu/IMP/IMP/-/issues/77MaxBin test data too small to give result2017-12-19T09:20:53+01:00Yohan Jaroszyohan.jarosz@uni.luMaxBin test data too small to give resultMaxBin test data on the imp runner is too small to produce results. So the test fails.
We need to provide better test data for that step. For now, the steps in the pipeline CI are set to `manual`MaxBin test data on the imp runner is too small to produce results. So the test fails.
We need to provide better test data for that step. For now, the steps in the pipeline CI are set to `manual`Shaman NarayanasamyShaman Narayanasamyhttps://git-r3lab.uni.lu/IMP/IMP/-/issues/13Handling multiple fastq files2017-12-19T09:20:54+01:00Shaman NarayanasamyHandling multiple fastq filesSometimes `fastq` files may not exist as a single pair of R1 and R2 files. They may exist as multiple pairs of fastq pairs. This is a potential request when we eventually release IMP to the public.
This may require a major refactor.
Sometimes `fastq` files may not exist as a single pair of R1 and R2 files. They may exist as multiple pairs of fastq pairs. This is a potential request when we eventually release IMP to the public.
This may require a major refactor.