Merge pull request #5698 from pjbriggs/trimmomatic

Trimmomatic

tools/trimmomatic/.shed.yml

@@ -0,0 +1,11 @@
+name: trimmomatic
+owner: pjbriggs
+description: A flexible read trimming tool for Illumina NGS data
+homepage_url: http://www.usadellab.org/cms/?page=trimmomatic
+long_description: |
+    Trimmomatic performs a variety of useful trimming tasks for
+    illumina paired-end and single ended data.8
+remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/main/packages/trimmomatic
+type: unrestricted
+categories:
+- Fastq Manipulation

tools/trimmomatic/README.rst

@@ -0,0 +1,125 @@
+Trimmomatic: flexible read trimming tool for Illumina NGS data
+==============================================================
+
+Galaxy tool wrapper for the Trimmomatic program, which provides various functions for
+manipluating Illumina FASTQ files (both single and paired-end).
+
+Trimmomatic has been developed within Bjorn Usadel's group at RWTH Aachen university
+http://www.usadellab.org/cms/index.php?page=trimmomatic
+
+The reference for Trimmomatic is:
+
+- Bolger, A.M., Lohse, M., & Usadel, B. (2014). Trimmomatic: A flexible trimmer
+  for Illumina Sequence Data. Bioinformatics, btu170.
+
+Controlling the available memory
+================================
+
+The default amount of memory avilable to trimmomatic is set to 8GB.
+To change the default amount of memory you can set the environment variable
+``_JAVA_OPTIONS`` to ``-Xmx<amount_of_memory_in_GB>G``. The recommended way to
+set this is in the job_conf.xml file. To change the available memory to 6GB, a
+line like the below should be added:
+
+``<env id="_JAVA_OPTIONS">-Xmx6G</env>``
+
+This will set the environment variable ``_JAVA_OPTIONS`` to ``-Xmx6G``.
+
+History
+=======
+
+============== ================================================================
+Version        Changes
+-------------- ----------------------------------------------------------------
+0.39+galaxy1   - Relocated to the ``tools-iuc`` repository
+0.39           - Update to Trimmomatic 0.39.
+0.38.1         - Bug fix: add dependency on ``coreutils`` so that
+                 ``readlink -e`` is supported across both Linux and MacOS
+                 platforms.
+0.38.0         - Update to Trimmomatic 0.38.
+0.36.6         - Added trimlog and log outputs; add support for
+                 ``fastqillumina`` and ``fastqsolexa`` input types
+0.36.5         - Remove tool_dependencies.xml and always use conda to resolve
+                 tool dependencies
+0.36.4         - Add option to provide custom adapter sequences for
+                 ILLUMINACLIP
+               - Add options ``minAdapterLength`` and ``keepBothReads`` for
+                 ILLUMINACLIP in palindrome mode
+0.36.3         - Fix naming of output collections. Instead of all outputs being
+                 called "Trimmomatic on collection NN" these will now be called
+                 "Trimmomatic on collection NN: paired" or "Trimmomatic on
+                 collection NN: unpaired".
+0.36.2         - Support fastqsanger.gz datatype. If fastqsanger.gz is used as
+                 input the output will also be fastqsanger.gz.
+               - Use $_JAVA_OPTIONS to customize memory requirements.
+0.36.1         - Reimplement to work with bioconda Trimmomatic 0.36 (toolshed
+                 version is still supported for now).
+0.36.0         - Update to Trimmomatic 0.36.
+0.32.4         - Add support for ``AVGQUAL`` and ``MAXINFO`` operations.
+0.32.3         - Add support for FASTQ R1/R2 pairs using dataset collections
+                 (input can be dataset collection, in which case tool also
+                 outputs dataset collections) and improve order and naming of
+                 output files.
+0.32.2         - Use ``GALAXY_SLOTS`` to set the appropriate number of threads
+                 to use at runtime (default is 6).
+0.32.1         - Remove ``trimmomatic_adapters.loc.sample`` and hard-code
+                 adapter files into the XML wrapper.
+0.32.0         - Add tool_dependencies.xml to install Trimmomatic 0.32
+                 automatically and set the environment.
+               - Update tool versioning to use Trimmomatic version number (i.e.
+                 ``0.32``) with tool iteration appended (i.e. ``.1``).
+0.0.4          - Specify '-threads 6' in <command> section.
+0.0.3          - Added MINLEN, LEADING, TRAILING, CROP and HEADCROP options of
+                 trimmomatic.
+0.0.2          - Updated ILLUMINACLIP option to use standard adapter sequences
+                 (requires the trimmomatic_adapters.loc file; sample version is
+                 supplied) plus cosmetic updates to wording and help text for
+                 some options.
+0.0.1          - Initial version
+============== ================================================================
+
+
+Credits
+=======
+
+This wrapper was originally developed and maintained by Peter Briggs
+(@pjbriggs).
+Peter van Heusden (@pvanheus) and Marius van den Beek (@mvdbeek) contributed 
+support for gz compressed FastQ files. Charles Girardot (@cgirardot) and
+Jelle Scholtalbers (@scholtalbers) contributed additional options to
+ILLUMINACLIP.
+Matthias Bernt (@bernt-matthias) added log and trimlog output.
+Nicola Soranzo (@nsoranzo) suggested using coreutils to enable cross-platform
+support across Linux and MacOS.
+Cristóbal Gallardo (@gallardoalba) updated Trimmomatic up to version 0.39.
+Peter Briggs wishes to acknowledge the help from Matthia Bernt
+(@bernt-matthias) with relocating the tool in the IUC tool repository,
+and the IUC for taking on responsibility for the tool.
+
+Developers
+==========
+
+The Trimmomatic tool is now maintained as part of the ``tools-iuc`` repository
+on GitHub:
+https://github.com/galaxyproject/tools-iuc/tools/tree/main/trimmomatic
+
+Licence (MIT)
+=============
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.

tools/trimmomatic/test-data/Illumina_SG_R1.fastq

@@ -0,0 +1,40 @@
+@MISEQ:1:000000000-A2Y1L:1:1101:19264:2433 1:N:0:NAAGGCGATAGATCGC
+AGATAGCCGAAGATAAAGAGNTCATAACCGTAAAGGCCAGAGACGAGAACCACTCGCAGGCAAGGTTTGCAAGCCTCGCCAAGAATATTATAGACCCGCTTGCCAACGACTGGCATTACATCACCGTAAAGAAGGTAGGCAAGAATCACTGGATCAGCATAACAGATGAGGGTAGAGACGCCGTATCGTTTCTGGGCTAGGTTATCTGGGCCGCCTTCTTGCGTCGGCGCACAGTCACAAAGGAAATGCC
++
+?????BBB@BBBB?BBFFFF#66EAFHHHCEFEDFGHHHHF@DFHACEEF@FDFHHHHEEEHHHF?FGEHFHDEFGHHCEHEFHHHHFFFCFDFFFFBEEEEEEEEEEEB?EEEEEEEEEEEBBEE?CE?:ACCC*??CAAEECE:?ECA:?A*?EEEE?EEEE?0AAC/?8)00**0:8'8;48*?8/8?AEEEE8:A*8*0:**0**:?C?480?EE?A#############################
+@MISEQ:1:000000000-A2Y1L:1:1101:18667:2435 1:N:0:NAAGGCGATAGATCGC
+ATATATTCATCCGCCATTATNAGAGTCCGATTACTTTAGAACAGTGCCGCGAATCCTTCGTCAACTGTAATCCAAGCGACATTGGTTCGATTAGCACGCATGAGGCACGAGATCTACGCGTATCTCTGGTAGATACACCAGGAGGGATGAGAGTTGAGCGAGTTAGCTGTGGCCAGAGAGATGGGTCTAATCGTAGTCTACAACTGGGAGTCACATGCCACTACCGACTAATCTGGTCGCCGAACGGGAG
++
+?????BBBDDDDADDDE@FF#66CFCFHHBEHHIIIHIIHHFHHGHHHHHHHHHHIHIHIFHHHHHHEGFHIHHIIIHHHHHHHHCFHHHHHHHFFFFFFEEEEFFEFEEBBEEEFFE@E8;EEFFFEF*:AEEEEEFFFEAAEA?A?ACAEF?CEEFED2<.?AAECEAEFEEE8??A8?CAAE1?EEE?AE*888AEEEEFEEFFA8A8?ACEAEEEAE?C:??ED2<E:C*:?*:8?ED<>8.)8?<
+@MISEQ:1:000000000-A2Y1L:1:1101:17523:2436 1:N:0:NAAGGCGATAGATCGC
+CATCACTACCGCTCAGGAATNTGACGGCAGTCTTAGCGGCGCTCTAGTGCGGGAGGCCGTATCTTGGAATAAGGTGTCGTCAAATGCAAGGCAGGTAACCCTACACGCCGAGGTTACCACTATACTCCCGTTTCTATATTCCTGTCTCTTATACACATCTCCGAGCCCACGAGACTAAGGCGAATATCGGTTGCCGTCTTCTGCTTGAAAAAAAAAAACAAACAAGAGAAGACGACGTACTGCACCACCA
++
+?<,<?BBBBBBBBBBBFFFF#6ACECCEC78CE=CGHEH7CHCHFGHADGHHHCCCHHE<DFHFFFFDFFFFFFDFDFDDEEEEEEEEECAEEEE;?BEEEBEEBCE;C;48;)?AACCEEE?AA?:?E88AEE:CE?AAEEEE:?***0:*??AAEEEEEEA?.8;E##################################################################################
+@MISEQ:1:000000000-A2Y1L:1:1101:15489:2437 1:N:0:NAAGGCGATAGATCGC
+GAGCAGTCGGGCTCAGCGCTNTGCAAATTCTAGTTAGAAACTCACAGTTCTGACAAGCCTTAGGTCAGTGTGATTGGCGGTTAGTCAACTCGGAGAAAGCGTCTTTTCCCGACTTGAATGGTTTGTCCCGACAGTTCGTTGACTGGGGTTTCGTCAGCCTTGAGCGGGGTTCCATCCATCTTTATCGCGCCTTGGGAAAGTAGTCGGCGGGCTTCGGGGTTGGGTGAGGGCAATCCTTGTTCGGTCAAAA
++
+5====>/<@@@@@@>@CCCE#66>ACEEEEGGGGGGGFFFEFDFFFFF=CDEFFFFEDEFFFFFC=AEBF-AA@CE;ECD5<5<==C==DEEE)83CD==@+4@DEE*<D1<)1@;888*90;*1988@)2)'4;=EE################################################################################################################
+@MISEQ:1:000000000-A2Y1L:1:1101:18851:2442 1:N:0:NAAGGCGATAGATCGC
+GGTATCCCCCGGCAGTGAGGATGGAGCCATGGTCTGCATCATACTCACCGTAGGTGAGAATATCCACGTCCTTCGACTCCTGGGTGCCGTCTATGGTGCCCTCTGTTACCAGGCAGTGACGGAGGACATGGTGAGGTTTCAGTACCTCTGGCCCGGCCTGGGTCACAGGGTCAGACTGGGTGACCTTCATGAAGCGTCTGGTGACGTAGCTGTGATAGTCCAGCTTGGCAACCTCTGCTGGTTGCAGAGG
++
+??,<?BBBDDDDDDD<FFF@FC;FFFBEFHHHCDDHHGHHHDGHHHFHHEA?EEAEEHDEFHHHHHFECFHHHFHDHEEHHCFH7CEFHDEHHCFHHFHHF=FFFDFDFFFFEEEEDDEFEEE<BBCEBCE,==AE1::AAEECEE*?*AAEFF??>D?)8):A8?EC?8***0*00:8?*)0*1:?CACC:AA?;)?EEFAEECE88*)1A*10*1:*1?:AC::A)*::*8ACEEE?###########
+@MISEQ:1:000000000-A2Y1L:1:1101:15290:2442 1:N:0:NAAGGCGATAGATCGC
+AAAATAATCCTAAAAAATAACCTCTATGCCGCCGAACGCTCCGCCTCTATCTTCGTAAAAACTATCTTCTCCTCCTCACCTCCATAATCAAGCATCAAGCGATCGCCCTCCGCCAACTCACCCCGCAAAATCTTATCCGCTAGCGGATTCTCAATCTCCGTCTGAATGACCCGCCTCAGCGGCCGCGCCCCATAAACCGAATCAAATCCACGCCTGTCTCTTATACACATCTCCGAGCCCACGAGACTAA
++
+?????BBBDDDDDDDDGGGGGGIIIHHFFHHHHHHHHHHEHHEHHHHHIIHHHHHFEHIIIHHIHHIHIHIIIIIHHHHHHHHHHHHHHHHDHHHHHHHHGEDFGGGGGGG;CEGEGCEGGGGG8>GGGGEGGEECEGGGGD8EDGGAEGEEGGCE:CGG8CEEGG???CEE<DG8CC*??>DG.8<AGGGGCEEG*C2<GCCECE*:?CE?CE9C:C:C:?C*1**010:*?E82'2<GCE########
+@MISEQ:1:000000000-A2Y1L:1:1101:18106:2444 1:N:0:NAAGGCGATAGATCGC
+GTAGTATTCTCATATCACAAGTCCCCAAACTGCATAAGGTGTGGAGTGGAGTGTCTCCCACTGCATTTTGTTGGTTTGGGTTGCATTTTTTGTGGCACAAAATTATCTTTAAACACTCTAAGCTCATATTTGCACATGCAACATGAATTGGAGCATTTCTTTTGCAGTCAACTGCCAGTACATTAACTCCACTCTGTAATAGTAAATCCTGTCTCTTATCCACATCTCCGAGCCCACGAGAATAAGGCGA
++
+55,,5?9BBBBB<<BBFFFFFFFHHFBEFHFHHHFDFCF0A9@>9D9DFG;FHHHHGHHFFFFHHHHECDCEFF>EFEEEE@CDFEFHHGHHHHEHDGHHFHDFHFHHHHFFHHH@FDD??DFFFFDBBEEBEEEEEEEEEEEEEEEEE,;?CEC;CEEEECB?CEEEEEEEECEEE?C?CE*0?***/:::?:*/?:A::**/:*:ACE?0:::A::***00::*/?C888??EEE#############
+@MISEQ:1:000000000-A2Y1L:1:1101:15892:2446 1:N:0:NAAGGCGATAGATCGC
+CTTCCCCACGGCCCAGACACAAGAGACGACCTCCATAAATCTTTTAGAGGGTGACCGCATCTCCGACGCAAACCAGGACGCCGATACCCTCGTGGTGGTGTTCGACCGTACGGATGGCGCAGACACCGACGGCACTAGTGCCACGGTATCAGGTACCACCATAACGTATGATTCGGGCACGCTCAAGGGCCAGCGTGACGGAATCGATAGAATACACTACACGGTGACTGATGGGGCCAGCCAAACCTGT
++
+?????BBBDBDDDDDDFFFFFFHIHIHHHHHHIHIFGGHFHHHHIIFHIHH?EEGHHHHHH-EGEHHCEHHHHH@FDFFEFF5@EEEFFEFE;AECCE;AEEEEEA?8?AEDDEEDFFDE2>>EEFF<<<2>D?DEEE*:C?AA<>8AEFCEE:?C?EEE?CEFEE0?:E?ACEECD8>EE>)8>E:CEEEEEED.)?AE??A?:A?*??:C0?CCE?AAA:88.88?::C:C?*8)4A?A#########
+@MISEQ:1:000000000-A2Y1L:1:1101:17903:2450 1:N:0:TAAGGCGATAGATCGC
+GTGCAGGGGGTGTGGTCAATCCACACTGTTGCTGAGGTGATTGGGTCTCCGGGGTCAACTCCATGAGGTAGCAGACCAGTGCCAGAGATAGTGACCACAGTGTTGGCCCTGTCTCTTATACACATCTCCGAGCCCACGAGACTAAGGCGAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAGACTTTTAAAAAACCGATCTACACCTTGACAGGCTATTAAAGGAAACTGGCCTGGTATCACAG
++
+=5===<>+5<5<+5=@CC;8CEEEEE;-8ACFDE.7C87CF-A>E>E=FFE**>>5AEDAEED-5-5AADC=D+=DDE<++3+CCD9DCD+=@3:DEEEEDD<@D*9DE99;@;@EE@;@@EEE7@@8@:@@@;9EE'449?<<E;=E<<;8(6;?##############################################################################################
+@MISEQ:1:000000000-A2Y1L:1:1101:15113:2451 1:N:0:TAAGGCGATAGATCGC
+TCTCAGATGAGCATGCAGCAGCCCAGACTCGCCCCACGCAGTTTGCCAACCACAAGGCCATCCTCGGCCTGTCAGCCTGCCCCTCCCTCCCTCACCAGCTAGCCTCCTATGCCGCGGTAGGGGGCTCAAAGAGATTCAGACACAGCCACGTAATCATGTTACTTGCCCATTCCCCCCTCCCTCCTCCTCCTCTCCCCCCCTCTCTTCCCCTCTCCCCTCCCCTCCTCCCCTCCTGTCCCTTATACACATC
++
+=,,<=>>>@@@@@9@@CCEE@EE+++6C8-++CECE+>DCC>@@EFFFFEEEDEE55+ACEF;-C+>EE++CBA--5A++CDC+4<<+=DE=CDEE@+@9D:D+4;@###############################################################################################################################################

tools/trimmomatic/test-data/Illumina_SG_R1.fastqillumina

@@ -0,0 +1,40 @@
+@MISEQ:1:000000000-A2Y1L:1:1101:19264:2433 1:N:0:NAAGGCGATAGATCGC
+AGATAGCCGAAGATAAAGAGNTCATAACCGTAAAGGCCAGAGACGAGAACCACTCGCAGGCAAGGTTTGCAAGCCTCGCCAAGAATATTATAGACCCGCTTGCCAACGACTGGCATTACATCACCGTAAAGAAGGTAGGCAAGAATCACTGGATCAGCATAACAGATGAGGGTAGAGACGCCGTATCGTTTCTGGGCTAGGTTATCTGGGCCGCCTTCTTGCGTCGGCGCACAGTCACAAAGGAAATGCC
++
+^^^^^aaa_aaaa^aaeeeeBUUd`egggbdedcefgggge_ceg`bdde_eceggggdddggge^efdgegcdefggbdgdeggggeeebeceeeeaddddddddddda^dddddddddddaadd^bd^Y`bbbI^^b``ddbdY^db`Y^`I^dddd^dddd^O``bN^WHOOIIOYWFWZSWI^WNW^`ddddWY`IWIOYIIOIIY^b^SWO^dd^`BBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+@MISEQ:1:000000000-A2Y1L:1:1101:18667:2435 1:N:0:NAAGGCGATAGATCGC
+ATATATTCATCCGCCATTATNAGAGTCCGATTACTTTAGAACAGTGCCGCGAATCCTTCGTCAACTGTAATCCAAGCGACATTGGTTCGATTAGCACGCATGAGGCACGAGATCTACGCGTATCTCTGGTAGATACACCAGGAGGGATGAGAGTTGAGCGAGTTAGCTGTGGCCAGAGAGATGGGTCTAATCGTAGTCTACAACTGGGAGTCACATGCCACTACCGACTAATCTGGTCGCCGAACGGGAG
++
+^^^^^aaacccc`cccd_eeBUUbebeggadgghhhghhggeggfgggggggggghghgheggggggdfeghgghhhggggggggbegggggggeeeeeeddddeededdaadddeed_dWZddeeedeIY`dddddeeed``d`^`^`b`de^bddedcQ[M^``dbd`dedddW^^`W^b``dP^ddd^`dIWWW`ddddeddee`W`W^`bd`ddd`d^bY^^dcQ[dYbIY^IYW^dc[]WMHW^[
+@MISEQ:1:000000000-A2Y1L:1:1101:17523:2436 1:N:0:NAAGGCGATAGATCGC
+CATCACTACCGCTCAGGAATNTGACGGCAGTCTTAGCGGCGCTCTAGTGCGGGAGGCCGTATCTTGGAATAAGGTGTCGTCAAATGCAAGGCAGGTAACCCTACACGCCGAGGTTACCACTATACTCCCGTTTCTATATTCCTGTCTCTTATACACATCTCCGAGCCCACGAGACTAAGGCGAATATCGGTTGCCGTCTTCTGCTTGAAAAAAAAAAACAAACAAGAGAAGACGACGTACTGCACCACCA
++
+^[K[^aaaaaaaaaaaeeeeBU`bdbbdbVWbd\bfgdgVbgbgefg`cfgggbbbggd[cegeeeeceeeeeecececcdddddddddb`ddddZ^adddaddabdZbZSWZH^``bbddd^``^Y^dWW`ddYbd^``ddddY^IIIOYI^^``dddddd`^MWZdBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+@MISEQ:1:000000000-A2Y1L:1:1101:15489:2437 1:N:0:NAAGGCGATAGATCGC
+GAGCAGTCGGGCTCAGCGCTNTGCAAATTCTAGTTAGAAACTCACAGTTCTGACAAGCCTTAGGTCAGTGTGATTGGCGGTTAGTCAACTCGGAGAAAGCGTCTTTTCCCGACTTGAATGGTTTGTCCCGACAGTTCGTTGACTGGGGTTTCGTCAGCCTTGAGCGGGGTTCCATCCATCTTTATCGCGCCTTGGGAAAGTAGTCGGCGGGCTTCGGGGTTGGGTGAGGGCAATCCTTGTTCGGTCAAAA
++
+T\\\\]N[______]_bbbdBUU]`bddddfffffffeeedeceeeee\bcdeeeedcdeeeeeb\`daeL``_bdZdbcT[T[\\b\\cdddHWRbc\\_JS_cddI[cP[HP_ZWWWIXOZIPXWW_HQHFSZ\ddBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+@MISEQ:1:000000000-A2Y1L:1:1101:18851:2442 1:N:0:NAAGGCGATAGATCGC
+GGTATCCCCCGGCAGTGAGGATGGAGCCATGGTCTGCATCATACTCACCGTAGGTGAGAATATCCACGTCCTTCGACTCCTGGGTGCCGTCTATGGTGCCCTCTGTTACCAGGCAGTGACGGAGGACATGGTGAGGTTTCAGTACCTCTGGCCCGGCCTGGGTCACAGGGTCAGACTGGGTGACCTTCATGAAGCGTCTGGTGACGTAGCTGTGATAGTCCAGCTTGGCAACCTCTGCTGGTTGCAGAGG
++
+^^K[^aaaccccccc[eee_ebZeeeadegggbccggfgggcfgggeggd`^dd`ddgcdegggggedbegggegcgddggbegVbdegcdggbeggegge\eeececeeeeddddccdeddd[aabdabdK\\`dPYY``ddbddI^I``dee^^]c^HWHY`W^db^WIIIOIOOYW^IHOIPY^b`bbY``^ZH^dde`ddbdWWIHP`IPOIPYIP^Y`bYY`HIYYIW`bddd^BBBBBBBBBBB
+@MISEQ:1:000000000-A2Y1L:1:1101:15290:2442 1:N:0:NAAGGCGATAGATCGC
+AAAATAATCCTAAAAAATAACCTCTATGCCGCCGAACGCTCCGCCTCTATCTTCGTAAAAACTATCTTCTCCTCCTCACCTCCATAATCAAGCATCAAGCGATCGCCCTCCGCCAACTCACCCCGCAAAATCTTATCCGCTAGCGGATTCTCAATCTCCGTCTGAATGACCCGCCTCAGCGGCCGCGCCCCATAAACCGAATCAAATCCACGCCTGTCTCTTATACACATCTCCGAGCCCACGAGACTAA
++
+^^^^^aaaccccccccffffffhhhggeeggggggggggdggdggggghhgggggedghhhgghgghghghhhhhggggggggggggggggcggggggggfdcefffffffZbdfdfbdfffffW]ffffdffddbdffffcWdcff`dfddffbdYbffWbddff^^^bdd[cfWbbI^^]cfMW[`ffffbddfIbQ[fbbdbdIY^bd^bdXbYbYbY^bIPIIOPOYI^dWQFQ[fbdBBBBBBBB
+@MISEQ:1:000000000-A2Y1L:1:1101:18106:2444 1:N:0:NAAGGCGATAGATCGC
+GTAGTATTCTCATATCACAAGTCCCCAAACTGCATAAGGTGTGGAGTGGAGTGTCTCCCACTGCATTTTGTTGGTTTGGGTTGCATTTTTTGTGGCACAAAATTATCTTTAAACACTCTAAGCTCATATTTGCACATGCAACATGAATTGGAGCATTTCTTTTGCAGTCAACTGCCAGTACATTAACTCCACTCTGTAATAGTAAATCCTGTCTCTTATCCACATCTCCGAGCCCACGAGAATAAGGCGA
++
+TTKKT^Xaaaaa[[aaeeeeeeeggeadegegggecebeO`X_]XcXcefZeggggfggeeeeggggdbcbdee]dedddd_bcedeggfggggdgcfggegcegeggggeeggg_ecc^^ceeeecaaddadddddddddddddddddKZ^bdbZbddddba^bddddddddbddd^b^bdIO^IIINYYY^YIN^Y`YYIINYIY`bd^OYYY`YYIIIOOYYIN^bWWW^^dddBBBBBBBBBBBBB
+@MISEQ:1:000000000-A2Y1L:1:1101:15892:2446 1:N:0:NAAGGCGATAGATCGC
+CTTCCCCACGGCCCAGACACAAGAGACGACCTCCATAAATCTTTTAGAGGGTGACCGCATCTCCGACGCAAACCAGGACGCCGATACCCTCGTGGTGGTGTTCGACCGTACGGATGGCGCAGACACCGACGGCACTAGTGCCACGGTATCAGGTACCACCATAACGTATGATTCGGGCACGCTCAAGGGCCAGCGTGACGGAATCGATAGAATACACTACACGGTGACTGATGGGGCCAGCCAAACCTGT
++
+^^^^^aaacacccccceeeeeeghghgggggghgheffgegggghheghgg^ddfggggggLdfdggbdggggg_eceedeeT_dddeededZ`dbbdZ`ddddd`^W^`dccddceecdQ]]ddee[[[Q]c^cdddIYb^``[]W`debddY^b^ddd^bdeddO^Yd^`bddbcW]dd]HW]dYbddddddcMH^`d^^`^Y`^I^^YbO^bbd^```YWWMWW^YYbYb^IWHS`^`BBBBBBBBB
+@MISEQ:1:000000000-A2Y1L:1:1101:17903:2450 1:N:0:TAAGGCGATAGATCGC
+GTGCAGGGGGTGTGGTCAATCCACACTGTTGCTGAGGTGATTGGGTCTCCGGGGTCAACTCCATGAGGTAGCAGACCAGTGCCAGAGATAGTGACCACAGTGTTGGCCCTGTCTCTTATACACATCTCCGAGCCCACGAGACTAAGGCGAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAGACTTTTAAAAAACCGATCTACACCTTGACAGGCTATTAAAGGAAACTGGCCTGGTATCACAG
++
+\T\\\[]JT[T[JT\_bbZWbdddddZLW`becdMVbWVbeL`]d]d\eedII]]T`dc`ddcLTLT``cb\cJ\ccd[JJRJbbcXcbcJ\_RYcddddcc[_cIXcdXXZ_Z_dd_Z__dddV__W_Y___ZXddFSSX^[[dZ\d[[ZWGUZ^BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+@MISEQ:1:000000000-A2Y1L:1:1101:15113:2451 1:N:0:TAAGGCGATAGATCGC
+TCTCAGATGAGCATGCAGCAGCCCAGACTCGCCCCACGCAGTTTGCCAACCACAAGGCCATCCTCGGCCTGTCAGCCTGCCCCTCCCTCCCTCACCAGCTAGCCTCCTATGCCGCGGTAGGGGGCTCAAAGAGATTCAGACACAGCCACGTAATCATGTTACTTGCCCATTCCCCCCTCCCTCCTCCTCCTCTCCCCCCCTCTCTTCCCCTCTCCCCTCCCCTCCTCCCCTCCTGTCCCTTATACACATC
++
+\KK[\]]]_____X__bbdd_ddJJJUbWLJJbdbdJ]cbb]__deeeedddcddTTJ`bdeZLbJ]ddJJba`LLT`JJbcbJS[[J\cd\bcdd_J_XcYcJSZ_BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB