Link contigs between assemblies

• Verification of the code and possible improvement maybe.
• See commit# 73dd1bc8 prepare_plot_files_w_metaspades.sh

changed milestone to %Greatness achieved

added Analysis label

added Clean Up label

Would transform that into Snakemake rules.

marked this issue as related to #33

changed milestone to %Analyses

marked this issue as related to #44 (closed)

Update: Since mmseqs2 provides only pairwise comparisons we might need a different approach.

New approach:

• concat all contigs into one FASTA
• run mmseq2 on this FASTA

Links:

• bioconda/mmseqs2 11.e1a1c
• repo
• wiki: clustering format

Giving up on that: tried easy-cluster and easy-linclust and was not able obtain reasonable results.

Better alternative to link contigs: MashMap

changed title from MMSEQS2: contig links to Link contigs between assemblies

mentioned in commit 015d6d47

marked this issue as related to #95 (closed)

marked this issue as related to #93 (closed)

changed milestone to %The bright future

Closing: one-to-one mapping is done using mashmap, see issue 95

closed