Metagenomes from Eastern Brazilian Amazonian floodplains in the wet and dry seasons¶

Narrative created by: Júlia B. Gontijo and Andressa M. Venturini

Brief sample description¶

Sediment samples from 0 to 10 cm depth were collected in triplicate from two floodplains of the Eastern Brazilian Amazon, one located on the Amazonas River (FP2, 2°28'11.2"S 54°38'49.9"W) and the other at the intersection between the Amazonas and the Tapajós rivers (FP3, 2°22'44.8"S 54°44'21.1"W), in the wet and dry seasons (May and October 2016, respectively). Total DNA was extracted in duplicate from 0.25 g of sediment using PowerLyzer PowerSoil DNA Isolation Kit. The metagenomic libraries were constructed using NEBNext Ultra II DNA Library Prep Kit for Illumina and paired-end sequenced (2 x 150 bp) on an Illumina HiSeq 2500 platform. Detailed information about the study sites, sampling, sediment physicochemical properties, DNA extraction and quantification have been previously described by Gontijo et al. (2021).

Sample IDs:
M1, M2 and M3: FP2, wet season
M4, M5 and M6: FP3, wet season
M7, M8 and M9: FP2, dry season
M10, M11 and M12: FP3, dry season

Table of Contents¶

1. Quality Evaluation of the Raw Reads

2. Raw reads filtering and trimming

3. Quality evaluation of the cleaned paired-end reads

4. Join overlapping paired-end reads

5. Quality evaluation of the joined reads

6. Taxonomic classification of the joined reads

7. References

1. Quality Evaluation of the Raw Reads

2. Raw reads filtering and trimming

3. Quality evaluation of the cleaned paired-end reads

4. Join overlapping paired-end reads

5. Quality evaluation of the joined reads

6. Taxonomic classification of the joined reads

Kaiju was run using three low abundance filters: 0.01%, 0.1%, and 1%. The results using the 0.01% filter were described in the announcement "Metagenomes from Eastern Brazilian Amazonian floodplains in the wet and dry seasons".

7. References

Gontijo JB, Paula FS, Venturini AM, Yoshiura CA, Borges CD, Moura JMS, Bohannan BJM, Nüsslein K, Rodrigues JLM, Tsai SM. 2021. Not just a methane source: Amazonian floodplain sediments harbour a high diversity of methanotrophs with different metabolic capabilities. Mol Ecol 30:2560–2572.

Created Object Name	Type	Description
M1_trimmed.PElib_paired	PairedEndLibrary	Trimmed Reads
M1_trimmed.PElib_unpaired_fwd	SingleEndLibrary	Trimmed Unpaired Forward Reads
M1_trimmed.PElib_unpaired_rev	SingleEndLibrary	Trimmed Unpaired Reverse Reads

Created Object Name	Type	Description
M2_trimmed.PElib_paired	PairedEndLibrary	Trimmed Reads
M2_trimmed.PElib_unpaired_fwd	SingleEndLibrary	Trimmed Unpaired Forward Reads
M2_trimmed.PElib_unpaired_rev	SingleEndLibrary	Trimmed Unpaired Reverse Reads

Created Object Name	Type	Description
M3_trimmed.PElib_paired	PairedEndLibrary	Trimmed Reads
M3_trimmed.PElib_unpaired_fwd	SingleEndLibrary	Trimmed Unpaired Forward Reads
M3_trimmed.PElib_unpaired_rev	SingleEndLibrary	Trimmed Unpaired Reverse Reads

Created Object Name	Type	Description
M4_trimmed.PElib_paired	PairedEndLibrary	Trimmed Reads
M4_trimmed.PElib_unpaired_fwd	SingleEndLibrary	Trimmed Unpaired Forward Reads
M4_trimmed.PElib_unpaired_rev	SingleEndLibrary	Trimmed Unpaired Reverse Reads

Created Object Name	Type	Description
M5_trimmed.PElib_paired	PairedEndLibrary	Trimmed Reads
M5_trimmed.PElib_unpaired_fwd	SingleEndLibrary	Trimmed Unpaired Forward Reads
M5_trimmed.PElib_unpaired_rev	SingleEndLibrary	Trimmed Unpaired Reverse Reads

Created Object Name	Type	Description
M6_trimmed.PE.lib_paired	PairedEndLibrary	Trimmed Reads
M6_trimmed.PE.lib_unpaired_fwd	SingleEndLibrary	Trimmed Unpaired Forward Reads
M6_trimmed.PE.lib_unpaired_rev	SingleEndLibrary	Trimmed Unpaired Reverse Reads

Created Object Name	Type	Description
M7_trimmed.PElib_paired	PairedEndLibrary	Trimmed Reads
M7_trimmed.PElib_unpaired_fwd	SingleEndLibrary	Trimmed Unpaired Forward Reads
M7_trimmed.PElib_unpaired_rev	SingleEndLibrary	Trimmed Unpaired Reverse Reads

Created Object Name	Type	Description
M8_trimmed.PElib_paired	PairedEndLibrary	Trimmed Reads
M8_trimmed.PElib_unpaired_fwd	SingleEndLibrary	Trimmed Unpaired Forward Reads
M8_trimmed.PElib_unpaired_rev	SingleEndLibrary	Trimmed Unpaired Reverse Reads

Created Object Name	Type	Description
M9_trimmed.PElib_paired	PairedEndLibrary	Trimmed Reads
M9_trimmed.PElib_unpaired_fwd	SingleEndLibrary	Trimmed Unpaired Forward Reads
M9_trimmed.PElib_unpaired_rev	SingleEndLibrary	Trimmed Unpaired Reverse Reads

Created Object Name	Type	Description
M10_trimmed.PElib_paired	PairedEndLibrary	Trimmed Reads
M10_trimmed.PElib_unpaired_fwd	SingleEndLibrary	Trimmed Unpaired Forward Reads
M10_trimmed.PElib_unpaired_rev	SingleEndLibrary	Trimmed Unpaired Reverse Reads

Created Object Name	Type	Description
M11_trimmed.PElib_paired	PairedEndLibrary	Trimmed Reads
M11_trimmed.PElib_unpaired_fwd	SingleEndLibrary	Trimmed Unpaired Forward Reads
M11_trimmed.PElib_unpaired_rev	SingleEndLibrary	Trimmed Unpaired Reverse Reads

Created Object Name	Type	Description
M12_trimmed.PElib_paired	PairedEndLibrary	Trimmed Reads
M12_trimmed.PElib_unpaired_fwd	SingleEndLibrary	Trimmed Unpaired Forward Reads
M12_trimmed.PElib_unpaired_rev	SingleEndLibrary	Trimmed Unpaired Reverse Reads

Created Object Name	Type	Description
M1_merged_joined	SingleEndLibrary	Joined Reads
M1_merged_unjoined	PairedEndLibrary	Unjoined Reads

Created Object Name	Type	Description
M2_merged_joined	SingleEndLibrary	Joined Reads
M2_merged_unjoined	PairedEndLibrary	Unjoined Reads

Created Object Name	Type	Description
M3_merged_joined	SingleEndLibrary	Joined Reads
M3_merged_unjoined	PairedEndLibrary	Unjoined Reads

Created Object Name	Type	Description
M4_merged_joined	SingleEndLibrary	Joined Reads
M4_merged_unjoined	PairedEndLibrary	Unjoined Reads

Created Object Name	Type	Description
M5_merged_joined	SingleEndLibrary	Joined Reads
M5_merged_unjoined	PairedEndLibrary	Unjoined Reads

Created Object Name	Type	Description
M6_merged_joined	SingleEndLibrary	Joined Reads
M6_merged_unjoined	PairedEndLibrary	Unjoined Reads

Created Object Name	Type	Description
M7_merged_joined	SingleEndLibrary	Joined Reads
M7_merged_unjoined	PairedEndLibrary	Unjoined Reads

Created Object Name	Type	Description
M8_merged_joined	SingleEndLibrary	Joined Reads
M8_merged_unjoined	PairedEndLibrary	Unjoined Reads

Created Object Name	Type	Description
M9_merged_joined	SingleEndLibrary	Joined Reads
M9_merged_unjoined	PairedEndLibrary	Unjoined Reads

Created Object Name	Type	Description
M10_merged_joined	SingleEndLibrary	Joined Reads
M10_merged_unjoined	PairedEndLibrary	Unjoined Reads

Created Object Name	Type	Description
M11_merged_joined	SingleEndLibrary	Joined Reads
M11_merged_unjoined	PairedEndLibrary	Unjoined Reads

Created Object Name	Type	Description
M12_merged_joined	SingleEndLibrary	Joined Reads
M12_merged_unjoined	PairedEndLibrary	Unjoined Reads

Metagenomes from Eastern Brazilian Amazonian floodplains in the wet and dry seasons¶

Brief sample description¶

Table of Contents¶

1. Quality Evaluation of the Raw Reads

2. Raw reads filtering and trimming

2. Raw reads filtering and trimming

3. Quality evaluation of the cleaned paired-end reads

4. Join overlapping paired-end reads

5. Quality evaluation of the joined reads

6. Taxonomic classification of the joined reads

7. References

Apps