feat: Emu support (#2792)

Add support for different sub commands of the [emu](https://github.com/treangenlab/emu) tool (species-level taxonomic abundance for 16S reads with long reads). I didn't add a wrapper for the build-database command because (1) I don't think it would be very useful (most cases do not involve a custom database, but a pre-built) and (2) the command is a bit complicated and I don't feel like they have a clear specifications of all the inputs you can add. ### QC I'm not sure what "* the `environment.yaml` pinning has been updated by running `snakedeploy pin-conda-envs environment.yaml` on a linux machine" means. I can commit the pin.txt file, for sure. But I'm not sure that is what the message means :) * [x] I confirm that: For all wrappers added by this PR, * there is a test case which covers any introduced changes, * `input:` and `output:` file paths in the resulting rule can be changed arbitrarily, * either the wrapper can only use a single core, or the example rule contains a `threads: x` statement with `x` being a reasonable default, * rule names in the test case are in [snake_case](https://en.wikipedia.org/wiki/Snake_case) and somehow tell what the rule is about or match the tools purpose or name (e.g., `map_reads` for a step that maps reads), * all `environment.yaml` specifications follow [the respective best practices](https://stackoverflow.com/a/64594513/2352071), * the `environment.yaml` pinning has been updated by running `snakedeploy pin-conda-envs environment.yaml` on a linux machine, * wherever possible, command line arguments are inferred and set automatically (e.g. based on file extensions in `input:` or `output:`), * all fields of the example rules in the `Snakefile`s and their entries are explained via comments (`input:`/`output:`/`params:` etc.), * `stderr` and/or `stdout` are logged correctly (`log:`), depending on the wrapped tool, * temporary files are either written to a unique hidden folder in the working directory, or (better) stored where the Python function `tempfile.gettempdir()` points to (see [here](https://docs.python.org/3/library/tempfile.html#tempfile.gettempdir); this also means that using any Python `tempfile` default behavior works), * the `meta.yaml` contains a link to the documentation of the respective tool or command, * `Snakefile`s pass the linting (`snakemake --lint`), * `Snakefile`s are formatted with [snakefmt](https://github.com/snakemake/snakefmt), * Python wrapper scripts are formatted with [black](https://black.readthedocs.io). * Conda environments use a minimal amount of channels, in recommended ordering. E.g. for bioconda, use (conda-forge, bioconda, nodefaults, as conda-forge should have highest priority and defaults channels are usually not needed because most packages are in conda-forge nowadays). --------- Co-authored-by: Filipe G. Vieira <1151762+fgvieira@users.noreply.github.com>
snakemake · Apr 12, 2024 · 149ef14 · 149ef14
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diff --git a/bio/emu/abundance/environment.linux-64.pin.txt b/bio/emu/abundance/environment.linux-64.pin.txt
@@ -0,0 +1,62 @@
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-64
+@EXPLICIT
+https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
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+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-h41732ed_0.conda#7aca3059a1729aa76c597603f10b0dd3
+https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-h7e041cc_5.conda#f6f6600d18a4047b54f803cf708b868a
+https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.10-4_cp310.conda#26322ec5d7712c3ded99dd656142b8ce
+https://conda.anaconda.org/conda-forge/noarch/tzdata-2024a-h0c530f3_0.conda#161081fc7cec0bfda0d86d7cb595f8d8
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h807b86a_5.conda#d211c42b9ce49aee3734fdc828731689
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+https://conda.anaconda.org/conda-forge/linux-64/biopython-1.83-py310h2372a71_0.conda#0128595946cebfaaf212cc45d4b9cd3c
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+https://conda.anaconda.org/bioconda/noarch/emu-3.4.5-hdfd78af_0.tar.bz2#34b067c6f82c3796a40e1b0ecaf094d3
diff --git a/bio/emu/abundance/environment.yaml b/bio/emu/abundance/environment.yaml
@@ -0,0 +1,6 @@
+channels:
+  - conda-forge
+  - bioconda
+  - nodefaults
+dependencies:
+  - emu=3.4.5
diff --git a/bio/emu/abundance/meta.yaml b/bio/emu/abundance/meta.yaml
@@ -0,0 +1,14 @@
+name: emu abundance
+description: Generate relative abundance estimates from ONT, Pac-Bio or short 16S reads using emu.
+url: https://github.com/treangenlab/emu
+authors:
+  - Curro Campuzano
+input:
+  - reads: single fastq file or paired fastq files
+  - db: emu database (optional; check documentation for pre-built databases and how to build them).
+output:
+  - abundances: TSV with relative (and optionally, absolute abundances).
+  - alignments: SAM file with the alignments (optional).
+  - unclassified: FASTA file with unclassified sequences (optional).
+params:
+  extra: Any optimal parameter such as --type (sequencer) or --min-abundance. Optional flags involving output are handled automatically (e.g. --output-dir, --output-basename ...)
diff --git a/bio/emu/abundance/test/Snakefile b/bio/emu/abundance/test/Snakefile
@@ -0,0 +1,30 @@
+rule abundance:
+    input:
+        reads="{sample}.fa",
+        db="database",
+    output:
+        abundances="{sample}_rel-abundance.tsv",
+        alignments="{sample}_emu_alignments.sam",
+        unclassified="{sample}_unclassified.fa",
+    log:
+        "logs/emu/{sample}_abundance.log",
+    params:
+        extra="--type map-ont --keep-counts",
+    threads: 3  # optional, defaults to 1
+    wrapper:
+        "master/bio/emu/abundance"
+
+
+rule abundance_paired:
+    input:
+        reads=["{sample}_R1.fq", "{sample}_R2.fq"],
+        db="database",
+    output:
+        abundances="{sample}_rel-abundance_paired.tsv",
+    log:
+        "logs/emu/{sample}_abundance_paired.log",
+    params:
+        extra="--type sr --keep-counts",
+    threads: 3  # optional, defaults to 1
+    wrapper:
+        "master/bio/emu/abundance"
diff --git a/bio/emu/abundance/test/database/species_taxid.fasta b/bio/emu/abundance/test/database/species_taxid.fasta
@@ -0,0 +1,15 @@
+>1:emu-silva:1 ['dada2-silva_1 Bacteria;Proteobacteria;Gammaproteobacteria;Pseudomonadales;Pseudomonadaceae;Pseudomonas;amygdali;']
+AACTGAAGAGTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAAG
+TCGAGCGGCAGCACGGGTACTTGTACCTGGTGGCGAGCGGCGGACGGGTGAGTAATGCCT
+AGGAATCTGCCTGGTAGTGGGGGATAACGCTCGGAAACGGACGCTAATACCGCATACGTC
+CTACGGGAGAAAGCAGGGGACCTTCGGGCCTTGCGCTATCAGATGAGCCTAGGTCGGATT
+AGCTAGTTGGTGAGGTAATGGCTCACCAAGGCGACGATCCGTAACTGGTCTGAGAGGATG
+ATCAGTCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAAT
+ATTGGACAATGGGCGAAAGCCTGATCCAGCCATGCCGCGTGTGTGAAGAAGGTCTTCGGA
+TTGTAAAGCACTTTAAGTTGGGAGGAAGGGCAGTTACCTAATACGTATCTGTTTTGACGT
+TACCGACAGAATAAGCACCGGCTAACTCTGTGCCAGCAGCCGCGGTAATACAGAGGGTGC
+GTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAA
+GCGCACNNNNGCGGTCTGTCAAGTCGGANGNNAAATCCCCGGGCTNNNNNNNGGAACTGC
+ATTCGAAACTGNCAGGCTTGAGTCTTGTAGAGGGNNNTNGNATTCNNNGTGTAGCGNNNN
+NNTGCGTAGAGATCTGGANGAACACCAGTGGCGAAGGCGGCTCTCTNGTCTGTAACTGAC
+GCTGAGGCTCGAAAGCNTGGGGAGCAAACAGGATTAGATANCCTGGTAGTCCACG
diff --git a/bio/emu/abundance/test/database/taxonomy.tsv b/bio/emu/abundance/test/database/taxonomy.tsv
@@ -0,0 +1,2 @@
+tax_id	superkingdom	phylum	class	order	family	genus	species
+1	Bacteria	Proteobacteria	Gammaproteobacteria	Pseudomonadales	Pseudomonadaceae	Pseudomonas	amygdali;
diff --git a/bio/emu/abundance/test/sample.fa b/bio/emu/abundance/test/sample.fa
@@ -0,0 +1,70 @@
+>Sphingobacterium_puteal_r1
+ACGGGTGCGTAACGCGTGAGCAACCTACCTCTATCAGGGGGATAGCCTCTCGAAAGAGAGATTAACACCGCATAACA
+TCAACAGTTCGCATGTTCGGTTGATTAAATATTTATAGGATAGAGATGGGCTCGCGTGACATTAGCTAGTTGGTAGGGTA
+ACGGCCTACCAAGGCGACGATGTCTAGGGGCTCTGAGAGGAGAATCCCCCACACTGGTACTGAGACACGGACCAGACTCC
+TACGGGAGGCAGCAGTAAGGAATATTGGTCAATGGGCGGAAGCCTGAACCAGCCATGCCGCGTGCAGGAAGACTGCCCTA
+TGGGTTGTAAACTGCTTTTGTCCAGGAATAAACCTCTTTACGTGTAGAGAGCTGAATGTACTGGAAGAATAAGGATCGGC
+TAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCG
+GCCTGTTAAGTCAGGGGTGAAATACGGTGGCTCAACCATCGCAGTGCCTTTGATACTGACGGGCTTGAATCCATTTGAAG
+TGGGCGGAATAAGACAAGTAGCGGTGAAATGCATAGATATGTCTTAGAACTCCGATTGCGAAGGCAGCTCACTAAGCTGG
+TATTGACGCTGATGCACGAAAGCGTGGGGATCGAACAGGATTAGATACCCTGGTAGTCCACGCCCTAAACGATGATAACT
+CGATGTTGGCGATAGACCGCCAGCGTCCAAGCGAAAGCGTTAAGTTATCCACCTGGGGAGTACGCCCGCAAGGGTGAAAC
+TCAAAGGAATTGACGGGGGCCCGCACAAGCGGAGGAGCATGTGGTTTAATTCGATGATACGCGAGGAACCTTACCCGGGC
+TTGAAAGTTAGTGAAGGATGCGGAGACGCATCCGTCCTTCGGGACACGAAACTAGGTGCTGCATGGCTGTCGTCAGCTCG
+TGCCGTGAGGTGTTGGGTTAAGTCCCGCAACGAGCGCAACCCCTATGTTTAGTTGCCAGCAAGTAATGTTGGGGACTCTA
+AACAGACTGCCTGCGCAAGCAGAGAGGAAGGTGGGGACGACGTCAAGTCATCATGGCCCTTACGTCCGGGGCTACACACG
+TGCTACAATGGATGGTACAGCGGGCAGCTACATAGCAATATGGTGCTAATCTCTAAAAGCCATTCACAGTTCGGATTGGG
+GTCTGCAACTCGACCCCATGAAGTTGGATTCGCTAGTAATCGCGTATCAGC
+>Sphingobacterium_puteal_r2
+GGCCTAATACATGCAAGTCGGACGGGATTTAAGTTAAAGCTTGCTTTAAGTTAATGAGAGTGG
+CGCACGGGTGCGTAACGCGTGAGCAACCTACCTCTATCAGGGGGATAGCCTCTCGAAAGAGAGATTAACACCGCATAACA
+TCAACAGTTCGCATGTTCGGTTGATTAAATATTTATAGGATAGAGATGGGCTCGCGTGACATTAGCTAGTTGGTAGGGTA
+ACGGCCTACCAAGGCGACGATGTCTAGGGGCTCTGAGAGGAGAATCCCCCACACTGGTACTGAGACACGGACCAGACTCC
+TACGGGAGGCAGCAGTAAGGAATATTGGTCAATGGGCGGAAGCCTGAACCAGCCATGCCGCGTGCAGGAAGACTGCCCTA
+TGGGTTGTAAACTGCTTTTGTCCAGGAATAAACCTCTTTACGTGTAGAGAGCTGAATGTACTGGAAGAATAAGGATCGGC
+TAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCG
+GCCTGTTAAGTCAGGGGTGAAATACGGTGGCTCAACCATCGCAGTGCCTTTGATACTGACGGGCTTGAATCCATTTGAAG
+TGGGCGGAATAAGACAAGTAGCGGTGAAATGCATAGATATGTCTTAGAACTCCGATTGCGAAGGCAGCTCACTAAGCTGG
+TATTGACGCTGATGCACGAAAGCGTGGGGATCGAACAGGATTAGATACCCTGGTAGTCCACGCCCTAAACGATGATAACT
+CGATGTTGGCGATAGACCGCCAGCGTCCAAGCGAAAGCGTTAAGTTATCCACCTGGGGAGTACGCCCGCAAGGGTGAAAC
+TCAAAGGAATTGACGGGGGCCCGCACAAGCGGAGGAGCATGTGGTTTAATTCGATGATACGCGAGGAACCTTACCCGGGC
+TTGAAAGTTAGTGAAGGATGCGGAGACGCATCCGTCCTTCGGGACACGAAACTAGGTGCTGCATGGCTGTCGTCAGCTCG
+TGCCGTGAGGTGTTGGGTTAAGTCCCGCAACGAGCGCAACCCCTATGTTTAGTTGCCAGCAAGTAATGTTGGGGACTCTA
+AACAGACTGCCTGCGCAAGCAGAGAGGAAGGTGGGGACGACGTCAAGTCATCATGGCCCTTACGTCCGGGGCTACACACG
+TGCTACAATGGATGGTACAGCGGGCAGCTACATAGCAATATGGTGCTAATCTCTAAAAGCCATTCACAGTTCGGATTGGG
+GTCTGCAACTCGACCCCATGAAGTTGGATTCGCTAGTAATCGCGTATCAGCAATGACGCGGTGAATACGTTCCCGGGCCT
+TGTACACA
+>Mycobacterium_saskatchewanense_r1
+AGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGGAAAGGTCTCTTCGGAGATAC
+TCGAGTGGCGAACGGGTGAGTAACACGTGGGCAATCTGCCCTGCACTTCGGGATAAGCCTGGGAAACTGGGTCTAATACC
+GGATAGGACCTTTAGGCGCATGCCTTTTGGTGGAAAGCTTTTGCGGTGTGGGATGGGCCCGCGGCCTATCAGCTTGTTGG
+TGGGGTGATGGCCTACCAAGGCGACGACGGGTAGCCGGCCTGAGAGGGTGTCCGGCCACACTGGGACTGAGATACGGCCC
+AGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCGACGCCGCGTGGGGGATGAC
+GGCCTTCGGGTTGTAAACCTCTTTCAGCAGGGACGAAGCGCAAGTGACGGTACCTGCAGAAGAAGCACCGGCCAACTACG
+TGCCAGCAGCCGCGGTAATACGTAGGGTGCGAGCGTTGTCCGGAATTACTGGGCGTAAAGAGCTCGTAGGTGGTTTGTCG
+CGTTGTTCGTGAAATCTCACGGCTTAACTGTGAGCGTGCGGGCGATACGGGCAGACTAGAGTACTGCAGGGGAGACTGGA
+ATTCCTGGTGTAGCGGTGGAATGCGCAGATATCAGGAGGAACACCGGTGGCGAAGGCGGGTCTCTGGGCAGTAACTGACG
+CTGAGGAGCGAAAGCGTGGGGAGCGAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGGTGGGTACTAGGTGTGG
+GTTTCCTTCCTTGGGATCCGTGCCGTAGCTAACGCATTAAGTACCCCGCCTGGGGAGTACGGCCGCAAGGCTAAAACTCA
+AAGGAATTGACGGGGGCCCGCACAAGCGGCGGAGCATGTGGATTAATTCGATGCAACGCGAAGAACCTTACCTGGGTTTG
+ACATGCACAGGACGCCGGCAGAGATGTCGGTTCCCTTGTGGCCTGTGTGCAGGTGGTGCATGGCTGTCGTCAGCTCGTGT
+CGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTCTCATGTTGCCAGCGGGTAATGCCGGGGACTCGTGAG
+AGACTGCCGGGGTCAACTCGGAGGAAGGTGGGGATGACGTCAAGTCATCATG
+>Streptococcus_sobrinus_r1
+AGTGTTACTAATGAGTCGCGAACGGGTGAGTAACGCGTAGGTAACCTGCCTGATAGCGGGGGATAACTATTGGAAACGAT
+AGCTAATACCGCATAAGAGGAGTTAACTCATGTTAACTGTTTAAAAGAAGCCATTGCTTCACTATCAGAGGACCTGCGT
+TGTATTAGCTAGTAGGTAGGGTAACGGCCTACCTAGGCAACGATACATAGCCGACCTGAGAGGGTGAACGGCCACACTGG
+GACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTAGGGAATCTTCGGCAATGGACGCAAGTCTGACCGAGCAACG
+CCGCGTGAGTGAAGACGGTTTTCGGATCGTAAAGCTCTGTTGTAGGGGAAGAACGTGTGTAAGAGTGGAAAGCTTACACA
+GTGACGGTACCCTACCAGAAAGGGACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTCCCGAGCGTTGTCCGG
+ATTTATTGGGCGTAAAGGGAGCGCAGGCGGTTTAGTAAGTCTGAAGTTAAAGGCATTGGCTCAACCAATGTATGCTTTGG
+AAACTGTTAGACTTGAGTGCAGAAGGGGAGAGTGGAATTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAGGAACAC
+CGGTGGCGAAAGCGGCTCTCTGGTCTGTCACTGACGCTGAGGCTCGAAAGCGTGGGTAGCGAACAGGATTAGATACCCTG
+GTAGTCCACGCCGTAAACGCTGAGTGCTAGGTGTTAGGTCCTTTCCGGGACTTAGTGCCGACGCTAACGCATTAAGCACT
+CCGCCTGGGGAGTACGACCGCAAGGTTGAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTA
+ATTCGAAGCAACGCGAAGAACCTTACCAGGTCTTGACATCCCGATGCCCGCTCTAGAGATAGAGTTTTTCTTCGGAACAT
+CGGAGACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTAT
+TGTTAGTTGCCATCATTAAGTTGGGCACTCTAGCGAGACTGCCGGTAATAAACCGGAGGAAGGTGGGGATGACGTCAAAT
+CATCATGCCCCTTATGACCTGGGCTACACACGTGCTACAATGGTTGGTACAACGAGTCGCAAGCCGGTGACGGCAAGCTA
+ATCTCTGAAAGCCAATCTCAGTTCGGATTGTAGGCTGCAACTCGCCTACATGAAGTCGGAATCGCTAGTAATCGCGGATC
+AGCACGCCGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCACGAGAGTTTGTAACACCCAAAGTCGGT
diff --git a/bio/emu/abundance/test/short_read_R1.fq b/bio/emu/abundance/test/short_read_R1.fq
@@ -0,0 +1,16 @@
+@SRR10391187.1 1 length=293
+GTGCCAGCCGCCGCGGTAATACGTAGGTGGCAAGCGTTGTCCGGAATTATTGGGCGTAAAGGGNTNNNNNNCGGTTCCTTAAGNNTGANNNNNNANCCCCCGGCTNNNNNNNGGAGNGTCNNNGGAANCTNNGGAACTTGAGTGCAGAAGAGGANNNNNNNNTNCNNNGTGTAGCNNNNNNNTGCGTAGAGATGTGNNNNNNCACCAGTGNNNANNNNGACTCTNNNNNNNGTAANTGNNNNTGNGNANCNAANNNNNNGGGAGCGNNNNNNNTTAGATANNNNNNNAGTACA
++SRR10391187.1 1 length=293
+CCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG#:######::CDFEGGGGGG##:CC######:#::?FGGGGF#######::BF#:BC###::BF#:B##::+BFFFGGFGGGGGFFGGGGF########6#6###86>FFGD#######66=CCEGCG?CGFF######*43BFGGC###3####*3/1;+#######*2;C#22####11#1#*#0#22######1131FE@#######(.04:A<#######(--(06
+@SRR10391187.2 2 length=293
+GTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTATCCGGAATTATTGGGCGTAAAGCGNGNNNNNNCGGTTTTTTAAGTNTGANNNNANAGCCCACGGCTNNNNNNNGGAGNGTCNNNGGAANCTNNAAAACTTGAGTGCAGAAGAGGANNNNNNNNTNCNNNGTGTAGCNNNNNNNTGCGCAGAGATATGGNNNNACACCAGTGNNGANNNNGACTTTNNNNNNNGTAANTGNNNNTGNTNTNCNAANNNNNNGGGATCANNNNGNNTTAGATANNNNNNNAGTCCA
++SRR10391187.2 2 length=293
+CCCCCGGGGGGGGGGGGGGGGGGFGGGFGGGGGGGGGGGGGGGGGGGGGGGDGFGGGGGGGGG#:######::DFDGGGGGGGG#:CD####:#:BFDGGGGGGG#######::DF#:BB###:8>D#::##8:=FEGGGGGGGGGGGGGACFG########6#6###86@FFGC#######*6>FGGGGGGGFGGG####31=CFGGGF##33####13=C>F#######/2;C#**####*1#*#/#.#22######1186*8>####0##(.08?F<#######(-4:FF
+@SRR10391187.3 3 length=295
+GTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGNANNNNNGCGGTCTGTCAAGTNGGANNNNAAATCCCCGGGCTNNNNNNNGGAACTGCNTTCGAAACTNNCAGGCTTGAGTCTTGTAGAGGGNNNGNGNATNCNNNGTGTAGCNNNNNNNAGCGTAGAGATCGGGANNNATACCGGTGGNGANNGCGGCCCCNNNNANNAAGAATGANGCTCAGNTGCGAANNNNNNGGGAGCANNNNGGATTAGATANNNNNNTAGCCCACG
++SRR10391187.3 3 length=295
+CCCCCGGGGGGGGGGGGGGGGGGGGGGGDGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGG#:#####::CDEGGGGGGGDG#:9C####::BDFGGGGGGGF#######:8BFGGFG#:BCFFGGG9##::>CGGGGGGGFGGGGGGGGGG###:#6#65#5###861>FF,#######**6@BCB>@CE9**43###341CF=DGC@#13##22**;CGG####*##22;**0+0#*19CF4#*/.:/C######/138C>@####00-4;4<:9:######)((-2<?<5
+@SRR10391187.4 4 length=295
+GTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACNNNNGCGGTCTGTCAAGTCGGANGNNAAATCCCCGGGCTNNNNNNNGGAACTGCATTCGAAACTGNCAGGCTTGAGTCTTGTAGAGGGNNNTNGNATTCNNNGTGTAGCGNNNNNNTGCGTAGAGATCTGGANGAACACCAGTGGCGAAGGCGGCTCTCTNGTCTGTAACTGACGCTGAGGCTCGAAAGCNTGGGGAGCAAACAGGATTAGATANCCTGGTAGTCCACG
++SRR10391187.4 4 length=295
+CCCCCGGGGGGGGGGGG@FGGGGEGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGEEGGGFGGGF####:,:DFGGGGGFGGGFGGC#:##::<DDGGGGGGGG#######::BFEFGGCGGGEFG7FGF#:B>FGGGGGFGGCGGGGGFFGG###:#6#6@FF###86DFGCFG######*6=CCCCEGGD,,2?+#/*3BEF>FGGGG58EGGGFGGGGGGG?#2:7<CCCGFC9CFGD*95C@C=5:=0)))#0/1723DD>F793556384,)-+#217CFFA<8A*6><