matam

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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...

loic-couderc

Ovgraphbuild major overhaul: Improve implementation speed ++

1

Change how reads pairs are sorted through by reading SAM file reference by reference and using a positions window gliding on each reference. One major problem: How to store read...

ppericard

- [ ] 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...

loic-couderc

Look into SGA scaffolding step if paired-end reads are used

1

Right now we do not use the scaffolding step since we treat all reads as single reads. Using paired-end reads could allow us to use the scaffolding step from SGA...

ppericard

Right now, all reads are treated as single reads. Some steps could benefit from using paired-end information (contigs assembly with SGA, MATAM scaffolding, ...). So we could still accept the...

ppericard

Paired-end reads could be used to help us chose between compatible contigs that are mapping on the same reference, thus allowing us to discriminate between 2 close species mapping on...

ppericard

BIOM format

3

Hi, Any chance of producing the results, i.e. abundance and taxonomy assignment, in BIOM format?

ycl6

SortMeRNA v2.1b now support them, so we also could in the future.

ppericard

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...

loic-couderc

When running index_default_ssu_rrna_db.py before building MATAM, SortMeRNA indexdb_rna executable is not found but indexing script terminates with no error... $ ./index_default_ssu_rrna_db.py 2017-01-30 11:26:01,604 - INFO - -- Get compressed archive...

ppericard