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I chose the following approach:
**after quality filtering**, each fastq file would be:
1. mapped using bowtie2 to the references in `references-for-removal.txt`
2. output sam file would be converte…
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sudo docker run --name test3 -v /home/ruplal/Documents:/home/ruplal/Documents -it haidyi/run_dbcan:latest python run_dbcan.py ./Documents/assembly.fa meta --out_dir ./Documents
ERROR: You missed so…
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Hello,
I tried to run canu in order to assemble bacterial metagenome with the following options (as suggest here : https://canu.readthedocs.io/en/latest/faq.html) :
`canu -p prefix -d canu/ ge…
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Hi,
I am mapping reads towards a big metagenome assembly. Total of 2,848,663,973 bp and the bt2 index files weight:
530M C_contigs.1.bt2
388M C_contigs.2.bt2
2.7M C_contigs.3.bt2
388M C_cont…
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Having some trouble with a missing output file for rule `get_read_stats` in `qc.snakefile`.
* I'm running atlas, version 2.0.1 installed via conda.
* I'm running on a local Linux server, 40 core…
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I've collected paired and single reads that were mapped to a metagenome-resolved bin, and I am now trying to reassemble the bin using either spades or metaspades.
I am running it on a machine with …
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fasta: http://gannet.fish.washington.edu/Atumefaciens/20190102_metagenomics_geo_megahit/megahit_out/final.contigs.fa
then use coverage file
http://gannet.fish.washington.edu/Atumefaciens/20190102…
sr320 updated
5 years ago
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Hi
I try to use SPAdes for a very big and divers metagenome assembly. But it crashes and gives the well known error:
```
19:26:05.527 295G / 564G INFO General (kmer_index_b…
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using
Megahit
https://github.com/voutcn/megahit
and/or
SPAdes
http://cab.spbu.ru/software/spades
sr320 updated
5 years ago
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Dear Silas,
Last time, I consulted you about the taxonomic and functional profiling for metagenomic data. After check the several papers and blocks, I want to try metaphlan2 and humann2 to get taxo…