Loïc Couderc
Loïc Couderc
Our Bioconda recipe does not use the same process to build MATAM. For maintenance purpose it will be better to use the same process.
**Is your feature request related to a problem? Please describe.** When the input FASTQ file does not exist, MATAM does not stop properly its execution **Describe the solution you'd like**...
RDP assign confidence scores at each level of the taxonomic hierarchy. For the moment this information is lost during the transformation to KRONA representation.
* Clustered db: #sequences & mean_length & min_length & max_length * Complete db: #sequences & mean_length & min_length & max_length
Currently, the tool used to cluster the database is Vsearch. It will be interesting to also provide sumaclust. Sumaclust: * Pro: Slightly better results * Cons: Slow Vsearch * Pro:...
When running matam_v1.3.0 with a depleted version of SILVA database, an error occured: ```bash 2017-10-16 13:26:24,198 - DEBUG - CMD: cat /workdir/lcouderc/data_matam/16S_rRNA/simulated_dataset/50x/matam/matam_v1.3.0_S128_SSURef_NR95_depleted_cov_50/genomes_complets.art_HS25_pe_1 01bp_50x.sortmerna_vs_SILVA_128_SSURef_NR95_b10_m10.scr_filt_geo_90pct.cov_filt_50.ovgb_i100_o50.cpts_N1_E1.read_metanode_component_taxo.tab | sort -T /workdir/lcouderc/data_matam/16S_r RNA/simulated_dataset/50x/matam/matam_v1.3.0_S128_SSURef_NR95_depleted_cov_50 -S 10000M...
- [ ] In debug mode, there is too much verbosity on the contigs assembly step. Restrict the logs to the assembly of the first component and the last one...
The read_fasta_file_handle function is duplicated in many locations: ```text scripts/compute_assembly_stats.py scripts/compute_lca_from_tab.py scripts/compute_pairwise_distance_matrix.py scripts/compute_ref_coverage_histogram.py scripts/exonerate_to_sam.py scripts/extract_taxo_from_fasta.py scripts/fasta_clean_name.py scripts/fasta_get_lengths.py scripts/fasta_length_filter.py scripts/fasta_name_filter.py scripts/filter_sam_by_coverage.py scripts/filter_sam_by_pid.py scripts/get_HMP_OTU_psn.py scripts/matam_assembly.py scripts/remove_redundant_sequences.py scripts/replace_Ns_by_As.py scripts/replace_Ns_by_rand_nu.py scripts/sort_fasta_by_length.py ``` The issue...