Loïc Couderc

Our bioconda recipe does not use the build.py script

1

Our Bioconda recipe does not use the same process to build MATAM. For maintenance purpose it will be better to use the same process.

Better error message when the input file does not exist

1

**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**...

Update krona visualization to take into account RDP confidence scores

1

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...