Alex Hübner

Spades-hammer stuck on reverse reads

5

When running metaspades on a paired-end FastQ files with error correction enabled, `spades-hammer` process through counting the k-mers on the forward reads, but gets stuck on doing the same on...

Add option to generate a nucl database from the Uniprot core proteins

5

Instead of downloading the protein sequences directly from Uniprot, this adds the possibility to retrieve the corresponding nucleotide sequences from ENA via metadata stored in XML format. It iterates over...

Hi everyone, First of all, thanks for keeping up the great work. I was wondering about the design philosophy that you chose for executing the PhyloPhlAn commands and whether using...

Set minimal contig length for metaBAT2 to 1,500 if the provided value is smaller

1

### Description of the bug The parameter `--min_contig_size` allows the user to specify the minimal contig length for binning and subsequent analysis. The program metaBAT2 requires a minimal contig length...

### Description of feature Currently, all contigs that were assembled by an assembler will be passed on to pyDamage when the `--ancient_dna` workflow is activated. However, from simulations we know...

Add support for single-end reads (in addition to paired-end reads)

8

### Description of feature Due to the high fragmentation of ancient DNA data, there is not much gain in using long-read DNA sequencing methods for assembling ancient DNA samples. However,...

Add option to split SPAdes read correction into separate process or enable SPAdes checkpoints

1

### Description of feature When running `metaSPAdes` as part of nf-core/mag, the first step is the read correction followed by the actual assembly steps. When using the sensible default resource...

Currently, nf-core/eager does only allow to extract reads that didn't align to the provided reference genome into a single FastQ file. While this is no issue when having merged overlapping...