feat: Emu support

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
+https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.2.2-hbcca054_0.conda#2f4327a1cbe7f022401b236e915a5fef
+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
+https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h807b86a_5.conda#d4ff227c46917d3b4565302a2bbb276b
+https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hd590300_5.conda#69b8b6202a07720f448be700e300ccf4
+https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.28.1-hd590300_0.conda#dcde58ff9a1f30b0037a2315d1846d1f
+https://conda.anaconda.org/conda-forge/linux-64/keyutils-1.6.1-h166bdaf_0.tar.bz2#30186d27e2c9fa62b45fb1476b7200e3
+https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.18-h0b41bf4_0.conda#6aa9c9de5542ecb07fdda9ca626252d8
+https://conda.anaconda.org/conda-forge/linux-64/libev-4.33-hd590300_2.conda#172bf1cd1ff8629f2b1179945ed45055
+https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.2-h7f98852_5.tar.bz2#d645c6d2ac96843a2bfaccd2d62b3ac3
+https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-13.2.0-ha4646dd_5.conda#7a6bd7a12a4bd359e2afe6c0fa1acace
+https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hd590300_0.conda#30fd6e37fe21f86f4bd26d6ee73eeec7
+https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b
+https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc
+https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-hd590300_5.conda#f36c115f1ee199da648e0597ec2047ad
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.4.20240210-h59595ed_0.conda#97da8860a0da5413c7c98a3b3838a645
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.2.1-hd590300_1.conda#9d731343cff6ee2e5a25c4a091bf8e2a
+https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.6-h166bdaf_0.tar.bz2#2161070d867d1b1204ea749c8eec4ef0
+https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20191231-he28a2e2_2.tar.bz2#4d331e44109e3f0e19b4cb8f9b82f3e1
+https://conda.anaconda.org/conda-forge/linux-64/libgfortran-ng-13.2.0-h69a702a_5.conda#e73e9cfd1191783392131e6238bdb3e9
+https://conda.anaconda.org/conda-forge/linux-64/libnghttp2-1.58.0-h47da74e_1.conda#700ac6ea6d53d5510591c4344d5c989a
+https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.45.2-h2797004_0.conda#866983a220e27a80cb75e85cb30466a1
+https://conda.anaconda.org/conda-forge/linux-64/libssh2-1.11.0-h0841786_0.conda#1f5a58e686b13bcfde88b93f547d23fe
+https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8228510_1.conda#47d31b792659ce70f470b5c82fdfb7a4
+https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_h4845f30_101.conda#d453b98d9c83e71da0741bb0ff4d76bc
+https://conda.anaconda.org/conda-forge/linux-64/zlib-1.2.13-hd590300_5.conda#68c34ec6149623be41a1933ab996a209
+https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.5-hfc55251_0.conda#04b88013080254850d6c01ed54810589
+https://conda.anaconda.org/bioconda/linux-64/bioawk-1.0-he4a0461_10.tar.bz2#3f4ea155f59ae781753ea76571e8564a
+https://conda.anaconda.org/bioconda/linux-64/k8-0.2.5-hdcf5f25_4.tar.bz2#d3c49a96ae45864706037702775ca7c2
+https://conda.anaconda.org/conda-forge/linux-64/krb5-1.21.2-h659d440_0.conda#cd95826dbd331ed1be26bdf401432844
+https://conda.anaconda.org/conda-forge/linux-64/libopenblas-0.3.27-pthreads_h413a1c8_0.conda#a356024784da6dfd4683dc5ecf45b155
+https://conda.anaconda.org/conda-forge/linux-64/python-3.10.14-hd12c33a_0_cpython.conda#2b4ba962994e8bd4be9ff5b64b75aff2
+https://conda.anaconda.org/conda-forge/linux-64/libblas-3.9.0-22_linux64_openblas.conda#1a2a0cd3153464fee6646f3dd6dad9b8
+https://conda.anaconda.org/conda-forge/linux-64/libcurl-8.7.1-hca28451_0.conda#755c7f876815003337d2c61ff5d047e5
+https://conda.anaconda.org/bioconda/linux-64/minimap2-2.28-he4a0461_0.tar.bz2#27d83cfe6bca3eb50aaeb6334371122d
+https://conda.anaconda.org/conda-forge/noarch/python-tzdata-2024.1-pyhd8ed1ab_0.conda#98206ea9954216ee7540f0c773f2104d
+https://conda.anaconda.org/conda-forge/noarch/pytz-2024.1-pyhd8ed1ab_0.conda#3eeeeb9e4827ace8c0c1419c85d590ad
+https://conda.anaconda.org/conda-forge/noarch/setuptools-69.2.0-pyhd8ed1ab_0.conda#da214ecd521a720a9d521c68047682dc
+https://conda.anaconda.org/conda-forge/noarch/six-1.16.0-pyh6c4a22f_0.tar.bz2#e5f25f8dbc060e9a8d912e432202afc2
+https://conda.anaconda.org/conda-forge/noarch/wheel-0.43.0-pyhd8ed1ab_1.conda#0b5293a157c2b5cd513dd1b03d8d3aae
+https://conda.anaconda.org/conda-forge/noarch/zipp-3.17.0-pyhd8ed1ab_0.conda#2e4d6bc0b14e10f895fc6791a7d9b26a
+https://conda.anaconda.org/conda-forge/noarch/importlib-metadata-7.1.0-pyha770c72_0.conda#0896606848b2dc5cebdf111b6543aa04
+https://conda.anaconda.org/conda-forge/linux-64/libcblas-3.9.0-22_linux64_openblas.conda#4b31699e0ec5de64d5896e580389c9a1
+https://conda.anaconda.org/conda-forge/linux-64/liblapack-3.9.0-22_linux64_openblas.conda#b083767b6c877e24ee597d93b87ab838
+https://conda.anaconda.org/conda-forge/linux-64/pathlib2-2.3.7.post1-py310hff52083_3.conda#62d26790749f62b9329425c901d93c3a
+https://conda.anaconda.org/conda-forge/noarch/pip-24.0-pyhd8ed1ab_0.conda#f586ac1e56c8638b64f9c8122a7b8a67
+https://conda.anaconda.org/bioconda/linux-64/pysam-0.22.0-py310h41dec4a_1.tar.bz2#19fdb9301a6debbb7fe9836670e3feb7
+https://conda.anaconda.org/conda-forge/noarch/python-dateutil-2.9.0-pyhd8ed1ab_0.conda#2cf4264fffb9e6eff6031c5b6884d61c
+https://conda.anaconda.org/conda-forge/noarch/flatten-dict-0.4.2-pyhd8ed1ab_1.tar.bz2#ccfb30b92adfeb283d4dcae3d0b6441b
+https://conda.anaconda.org/conda-forge/linux-64/numpy-1.26.4-py310hb13e2d6_0.conda#6593de64c935768b6bad3e19b3e978be
+https://conda.anaconda.org/conda-forge/linux-64/biopython-1.83-py310h2372a71_0.conda#0128595946cebfaaf212cc45d4b9cd3c
+https://conda.anaconda.org/conda-forge/linux-64/pandas-2.2.1-py310hcc13569_0.conda#cf5d315e3601a6a2931f63aa9a84dc40
+https://conda.anaconda.org/bioconda/noarch/emu-3.4.5-hdfd78af_0.tar.bz2#34b067c6f82c3796a40e1b0ecaf094d3

bio/emu/abundance/environment.yaml

@@ -0,0 +1,6 @@
+channels:
+  - conda-forge
+  - bioconda
+  - nodefaults
+dependencies:
+  - emu=3.4.5

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 ...)

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"

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

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;

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

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><