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### Discussed in https://github.com/wwood/CoverM/discussions/120
Originally posted by **kevinmyers** June 28, 2022
I have a set of 217 MAGs that I would like to use coverM to determine the ove…
wwood updated
2 years ago
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Hello,
I'm trying out DAMAPPER for mapping a set of unitigs to PacBio reads, and when parsing the results I notice that sometimes duplicate alignments to different parts of the same read are reporte…
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In the new_mbg/bonobo folder, there are 36 t2t scaffolds in the original MBG version vs 24 w/new. The files t2t_scaffolds_by_chr list the t2t scaffolds and their chromosome IDs. These both used trio-s…
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Using BWA MEM to map WGS reads to metagenomic contigs, it is possible to find no reads mapping to a small number of short contigs. This then results in inferring contig coverages of zero and an inabil…
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I get a segfault when setting `--soloFeatures SJ`. I have the most recent version, 2.7.10a_alpha_220818.
In detail:
1) If I set `--soloFeatures Gene GeneFull SJ` I get a segfault. `Log.out` has …
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Hello,
I have run the following commands:
minimap2 -x ava-ont -t32 reads.fastq reads.fastq -K5M | gzip -1 > n_reads.paf.gz
[M::mm_idx_gen::0.754*0.99] collected minimizers
[M::mm_idx_gen::0.858…
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For example: https://github.com/vgteam/vg#mapping
```
If your graph is large, you want to use vg index to store the graph and vg map to align reads. vg map implements a kmer based seed and extend ali…
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I like to combine different metagenome-assembled genomes (contigs) into one.
I tried to use miniasmwith:
```
cat all_genomes/*.fasta > x.fasta
minimap2 -x asm10 -t4 x.fasta x.fasta | gzip -…
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## Problem description
Currently (version 0.2.0-beta2), `flye_end_repair.sh` is run after the assembly step to fix any potential issues with the region around the ends of circular contigs. At the end…
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Hi,
I am trying to assemble the genome of a worm, and I was hoping that minipolish would detect the mitochondrial genome and output it in the gfa file.
I have sequencing one of my worm species a l…