Commit 6d127999 authored by Charles Girardot's avatar Charles Girardot

added new module for Drop-seq support. This 'dropseq' clips barcode and

UMI from read 1 and adds them to read2 headers
parent e1bdeefc
......@@ -3,7 +3,7 @@
<modelVersion>4.0.0</modelVersion>
<groupId>Je</groupId>
<artifactId>Je</artifactId>
<version>1.0</version>
<version>1.1</version>
<name>Je</name>
<description>Je provides command line utilities to deal with barcoded FASTQ files with or without Unique Molecular Index (UMI)</description>
......
../../dist/je
\ No newline at end of file
#!/bin/sh
# Wrapper around je_1.0_bundle.jar
# where are we stored ?
DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
# echo $DIR
# path to jar file to execute, this jar is supposed to be in the same dir as this script
JAR_FILE=$DIR"/je_1.0_bundle.jar"
# set default _JAVA_OPTIONS
_JAVA_OPTIONS=${_JAVA_OPTIONS:-'-Xmx4G -Xms256m'}
export _JAVA_OPTIONS
# uncomment to change logging level using your own log4j.xml found in $DIR file
# OPTS="-Dlog4j.configuration=file:$DIR/log4j.xml"
java $OPTS -jar $JAR_FILE "$@"
exit $?
../../dist/je_1.0_bundle.jar
\ No newline at end of file
......@@ -27,6 +27,7 @@ import java.util.Set;
import java.util.TreeSet;
import org.embl.cg.utilitytools.utils.StringUtil;
import org.embl.gbcs.je.dropseq.Jedropseq;
import org.embl.gbcs.je.jeclipper.Jeclipper;
import org.embl.gbcs.je.jeduplicates.MarkDuplicatesWithMolecularCode;
import org.embl.gbcs.je.jemultiplexer.Jemultiplexer;
......@@ -47,6 +48,7 @@ public class Je {
private static Logger log = LoggerFactory.getLogger(Je.class);
public static final String COMMAND_DROPSEQ = "dropseq";
public static final String COMMAND_CLIP = "clip";
public static final String COMMAND_DUPES = "markdupes";
public static final String COMMAND_MULTIPLEX = "demultiplex";
......@@ -59,6 +61,7 @@ public class Je {
ALLOWED_COMMANDS.add(COMMAND_DUPES);
ALLOWED_COMMANDS.add(COMMAND_MULTIPLEX);
ALLOWED_COMMANDS.add(COMMAND_MULTIPLEX_ILLUMINA);
ALLOWED_COMMANDS.add(COMMAND_DROPSEQ);
}
......@@ -111,6 +114,9 @@ public class Je {
else if(option.equalsIgnoreCase(COMMAND_DUPES)){
new MarkDuplicatesWithMolecularCode().instanceMainWithExit(argv);
}
else if(option.equalsIgnoreCase(COMMAND_DROPSEQ)){
new Jedropseq().instanceMainWithExit(argv);
}
else{
System.err.println(
"FATAL : We just reached a supposedly unreachable part of the code. Please report this bug to Je developpers indicating the options you used i.e. : \n "+
......@@ -128,6 +134,7 @@ public class Je {
+"\t "+COMMAND_MULTIPLEX+" \t\t demultiplex fastq file(s), with optional handling of molecular barcodes for further use in 'dupes' module\n"
+"\t "+COMMAND_MULTIPLEX_ILLUMINA+" \t demultiplex fastq file(s) using Illumina Index files, with optional handling of molecular barcodes for further use in 'dupes' module\n"
+"\t "+COMMAND_DUPES+" \t\t removes read duplicates based on molecular barcodes found in read name headers (as produced by clip or plex)\n"
+"\t "+COMMAND_DROPSEQ+" \t\t clips cell barcode and UMI from read 1 and adds them to header of read 2. This command is for processing drop-seq results.\n"
+"\n"
+"Version : "+getVersion()
;
......
This diff is collapsed.
/*
* The MIT License
*
* Copyright (c) 2009 The Broad Institute
*
* 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.
*/
package org.embl.gbcs.je.jedropseq;
import java.io.File;
import java.net.URISyntaxException;
import org.apache.log4j.Logger;
import org.embl.gbcs.je.dropseq.Jedropseq;
import org.embl.gbcs.je.jeclipper.Jeclipper;
import org.junit.After;
import org.junit.Assert;
import org.junit.Before;
import org.junit.Test;
public class JedropseqTest {
private static Logger log = Logger.getLogger(JedropseqTest.class);
static final String READ1_FILENAME = "dropseq_test_read1.txt";
static final String READ2_FILENAME = "dropseq_test_read2.txt";
static final String RES_FILENAME = "dropseq_test_read1_tagged.txt";
//@After
public void cleanUpResultFiles(){
try {
File f1 = new File(JedropseqTest.class.getResource(READ1_FILENAME).toURI());
File outdir = f1.getParentFile();
String [] fnames = new String []{
RES_FILENAME
};
for (String fname : fnames) {
File f = new File(outdir, fname) ;
if(f.exists()){
f.delete();
}
}
log.info("Test Env. Cleanup done");
} catch (URISyntaxException e) {
throw new RuntimeException("Test Env. Tear Down : Cleanup failed");
}
}
@Before
public void cleanUpLeftOverResultFiles(){
cleanUpResultFiles();
}
@Test
public void testClipper(){
try {
File f1 = new File(JedropseqTest.class.getResource(READ1_FILENAME).toURI());
File f2 = new File(JedropseqTest.class.getResource(READ2_FILENAME).toURI());
File res = new File(f1.getParent(), RES_FILENAME);
//File res = new File( RES_FILENAME);
String[] argv = new String[] {
"F1="+f1.getAbsolutePath(),
"F2="+f2.getAbsolutePath(),
"LEN=12",
"ULEN=8",
"O="+ res.getAbsolutePath(),
"GZ=false"
};
Jedropseq j = new Jedropseq();
Assert.assertFalse(j.TEST_MODE_STOP_AFTER_PARSING);
//parse
Assert.assertEquals(0, j.instanceMain(argv));
} catch (URISyntaxException e) {
throw new RuntimeException(e);
}
}
}
@MISEQ:541:000000000-ANU7K:1:1101:17616:1531 1:N:0:
CCCCTTTCTTCTTTTGTTCC
+
1>1111B1B3BFB311B133
@MISEQ:541:000000000-ANU7K:1:1101:16613:1555 1:N:0:
CGGCGTGGTGATGAAGTTTT
+
A1AA?DA?111D331BFFGG
@MISEQ:541:000000000-ANU7K:1:1101:14966:1558 1:N:0:
GGCTTACTACAACAACCCTT
+
111>>11B3@11B111AAFG
@MISEQ:541:000000000-ANU7K:1:1101:16558:1569 1:N:0:
CGTTACCTGTAGTAACAGGC
+
>1AA1ABFBF33FD3F111A
@MISEQ:541:000000000-ANU7K:1:1101:17288:1571 1:N:0:
TGTCGCTTCACTAGATGCGT
+
A1>A1>AAAFFFF11F3A1E
@MISEQ:541:000000000-ANU7K:1:1101:14146:1573 1:N:0:
TCACCCCATCCATGCTTGAT
+
A1>>>?A1B111G31FF11B
@MISEQ:541:000000000-ANU7K:1:1101:16878:1574 1:N:0:
ACTGCTAGTTGAACGGCAAA
+
11>11B11BD13BCA1E100
@MISEQ:541:000000000-ANU7K:1:1101:17254:1575 1:N:0:
CCCGTTGTCCCAAACTACTT
+
1111>1111B111A1B11AD
@MISEQ:541:000000000-ANU7K:1:1101:16027:1578 1:N:0:
CCCCTTTCACATGCAAACGG
+
1>>>AFFFBD3D1C111B11
@MISEQ:541:000000000-ANU7K:1:1101:14893:1580 1:N:0:
TCAGACTAGCCAAGCCCATC
+
>1111BC11>B1A1AF11BG
@MISEQ:541:000000000-ANU7K:1:1101:17897:1584 1:N:0:
TCCGCGTCAGCTGCGGGGGC
+
A11111>11>BD1A000/AA
@MISEQ:541:000000000-ANU7K:1:1101:16149:1585 1:N:0:
GCCGACTACCGATTGCGAGC
+
11111>>1BC11AE010000
@MISEQ:541:000000000-ANU7K:1:1101:13135:1586 1:N:0:
CTGAGGAGATTCGTTGATAT
+
>11>1111>FFFAGGF1BEG
@MISEQ:541:000000000-ANU7K:1:1101:17163:1595 1:N:0:
CTGTAAGTCTCTAGATCATT
+
>11>1@3DFFFFGGFGFFGG
@MISEQ:541:000000000-ANU7K:1:1101:15599:1597 1:N:0:
TTATCGCTCGTCCAGGCTGG
+
AA1A>>AF?1>111110B00
@MISEQ:541:000000000-ANU7K:1:1101:13575:1598 1:N:0:
CCATCCAGGGTATCGGACGT
+
A11AACC111CCGG?E1A0E
@MISEQ:541:000000000-ANU7K:1:1101:17008:1599 1:N:0:
CTGTCTCCCATCATCCTGAT
+
>11>1DDFFBDCGFFGGCFG
@MISEQ:541:000000000-ANU7K:1:1101:14913:1599 1:N:0:
TCTCCCATTCACCTGTCTCT
+
A1AAAC>DFDFFFG1GCGGG
@MISEQ:541:000000000-ANU7K:1:1101:14307:1601 1:N:0:
CCCTTTCTTGAGATCAGTAT
+
A1>>AF13@13@13AG1A3B
@MISEQ:541:000000000-ANU7K:1:1101:18212:1601 1:N:0:
TCAGACTAGCCAACAATGGG
+
>>1>11B1CC11EFCAGBCA
@MISEQ:541:000000000-ANU7K:1:1101:16530:1602 1:N:0:
CACTCAGGCTTGGGGATTTT
+
>1>A1111BFF?1C?A1FEG
@MISEQ:541:000000000-ANU7K:1:1101:13045:1602 1:N:0:
GTTGAAGGGGAATCACCGGC
+
>>A>3554ADB?GGGGF?EG
@MISEQ:541:000000000-ANU7K:1:1101:15570:1602 1:N:0:
GATTCCTAATGCGGCAGTTT
+
>3>AABFFFFFFC2A2AFGG
@MISEQ:541:000000000-ANU7K:1:1101:14068:1602 1:N:0:
GACTGCTCCATTAAAGGACC
+
>1>A1B3BFFFFF3FF11BC
@MISEQ:541:000000000-ANU7K:1:1101:13869:1603 1:N:0:
TTTCCTTTCCTCATCGGTCT
+
>11>1BDFFDFFDGF11EAE
@MISEQ:541:000000000-ANU7K:1:1101:17054:1605 1:N:0:
TTCTATCCTTACGAAGGGAT
+
AA>AAFFFFFB11A1111AF
@MISEQ:541:000000000-ANU7K:1:1101:16556:1607 1:N:0:
TCACCCCATCCAGGCTTATG
+
A1>AAF?1B1CBAFGGG111
@MISEQ:541:000000000-ANU7K:1:1101:18064:1607 1:N:0:
CCACGCGATGATCTCAACTG
+
1111>A11A1DFFGGBBBGB
@MISEQ:541:000000000-ANU7K:1:1101:16786:1609 1:N:0:
TCCCGTTAACTCTGTGTAAT
+
A1>>1AF>AFFFGGGCGG3F
@MISEQ:541:000000000-ANU7K:1:1101:14609:1610 1:N:0:
GTGCCTAATAATTAGATTGC
+
A33>>FFFFBDFG6A5BGFG
@MISEQ:541:000000000-ANU7K:1:1101:13501:1611 1:N:0:
CCGCATCTCTATTTCCTCCC
+
A3>A3AAFFFBFGGGGGGGF
@MISEQ:541:000000000-ANU7K:1:1101:14327:1611 1:N:0:
GTCGGAGTTAATCGCTTTTA
+
>>A1111>F3DDGGFGGGF3
@MISEQ:541:000000000-ANU7K:1:1101:13178:1611 1:N:0:
ATTGATAATGCGTGTAGCGT
+
>1>>1D33F3DAECEG1FEF
@MISEQ:541:000000000-ANU7K:1:1101:17881:1612 1:N:0:
CCATCCAGGGTTGGAACGTT
+
>1>>111111BBA1EFA1A0
@MISEQ:541:000000000-ANU7K:1:1101:16279:1613 1:N:0:
CCTCGTTCTGATGGAGTCAC
+
A>AA3AAFB5BDBBC4FG5G
@MISEQ:541:000000000-ANU7K:1:1101:13531:1614 1:N:0:
GTCTTACTACAGCACCCGTG
+
11>A1B1DDB11FCGGAEE?
@MISEQ:541:000000000-ANU7K:1:1101:18008:1614 1:N:0:
CGGCACATCAACCGGATGCT
+
11>11>1B11BFFE1E00BG
@MISEQ:541:000000000-ANU7K:1:1101:13221:1614 1:N:0:
CTAGGCATCACACTCACGGT
+
AA3>3FFFFFFFGGGFF4EF
@MISEQ:541:000000000-ANU7K:1:1101:16820:1614 1:N:0:
TCAGACTAGCCACTCAAGGC
+
A11>?FF1B1FFGFFF11BF
@MISEQ:541:000000000-ANU7K:1:1101:14981:1615 1:N:0:
TGGCCTTTGATGTAAGTACT
+
A11AAFFFF3FFGGGGGGDG
@MISEQ:541:000000000-ANU7K:1:1101:14408:1615 1:N:0:
GTGTTGGACAGTGGCCCTTT
+
111>A?1@B11BBCCF1AGG
@MISEQ:541:000000000-ANU7K:1:1101:16414:1616 1:N:0:
GGGTTGCACAGGAGCATGTT
+
111>A1C1D111B1F1F1FG
@MISEQ:541:000000000-ANU7K:1:1101:17385:1617 1:N:0:
TTTTGTCAACGAAAGAGACG
+
AAAA1CB33BAAFEGFB1C0
@MISEQ:541:000000000-ANU7K:1:1101:15349:1617 1:N:0:
ATATACGTCCGCGAGAGCGC
+
>>3A3B>DFAA@ECGFGC2E
@MISEQ:541:000000000-ANU7K:1:1101:16880:1617 1:N:0:
TCAGCCTAGCCAGGTTCCCG
+
>>1>11C11@>@A11FACFE
@MISEQ:541:000000000-ANU7K:1:1101:16619:1618 1:N:0:
TCGCAGAATCAAGGCCCCCC
+
A>1>1111DFFF11AG11AE
@MISEQ:541:000000000-ANU7K:1:1101:18040:1618 1:N:0:
CTTCGATAAGCTTGAGGATT
+
AAAA1>D?ABFFGFAFF1FG
@MISEQ:541:000000000-ANU7K:1:1101:17608:1619 1:N:0:
GCACACGCGCCGACAAAACT
+
111>1B111>D?EGEEFAFG
@MISEQ:541:000000000-ANU7K:1:1101:12988:1619 1:N:0:
ACCCATGCATCCGCGCAACT
+
>1>A1F11DFFBAFGGCCCG
@MISEQ:541:000000000-ANU7K:1:1101:17675:1620 1:N:0:
CTTCGTATATGGCGTGGGTA
+
>AAA1C1CFBF1FE1E10A1
@MISEQ:541:000000000-ANU7K:1:1101:17616:1531 2:N:0:
CTCATTTTTTTTTTTCTACTCTTCTTTTCTCCTTCTCCCTCCTTTCCTTCCT
+
11111333B11000001222121121112A21A11111000/0121112101
@MISEQ:541:000000000-ANU7K:1:1101:16613:1555 2:N:0:
CTATAAGCTCATTACTCCATCCGTTTTCTCTGCGCTCCTCTCCTTTCTCTCT
+
1>1>133BDF1BF3AGGA11111A100BABD3100000B01001BAA22211
@MISEQ:541:000000000-ANU7K:1:1101:14966:1558 2:N:0:
CTCGCAGGAGTGCCCGCGACTTTGCCGCCTCCCACCACTCCCCTCCTCCTGC
+
1>>111>11>BCA11A000AA0111A///A///00///AB0//0/ABAA011
@MISEQ:541:000000000-ANU7K:1:1101:16558:1569 2:N:0:
TGCTGAGGCGTGCCTATCCCTCTTTCCTTTGTTTTTTCTCCTCCTTTCTCTC
+
111>11B>>1>11011B1011001321122120A00/0121A000A2A222B
@MISEQ:541:000000000-ANU7K:1:1101:17288:1571 2:N:0:
GCATGGGACAGTACTCTGCGTTTCTTCAAAATTTACCCTACCCTCCCCTCCC
+
11>>1111B11B3AGFF311A001A3D31311112210100001////0///
@MISEQ:541:000000000-ANU7K:1:1101:14146:1573 2:N:0:
CTGCGTTGATACCAAAAAAATTTAAAAAAAAAATTACTTAAATTTCATTTTT
+
>A>A1>AD@FFFG1FFA100011221A10////01112221122122222B@
@MISEQ:541:000000000-ANU7K:1:1101:16878:1574 2:N:0:
TTACTAAGTCCATTCCTTGATCCCCCTCTTTCGTCAAACTTCTCCAGTATTA
+
1>1>AD3B33@3EDF3B311B11A1A000A3300B00111122111A21A22
@MISEQ:541:000000000-ANU7K:1:1101:17254:1575 2:N:0:
GCGTGACTGTGTCAACTGGGTATTCTTCTTTTTCTTTTCTCTTTCTCACCCT
+
111>1113111BB331B111B1133333313110133131222122221000
@MISEQ:541:000000000-ANU7K:1:1101:16027:1578 2:N:0:
GTGAATGGGGGTACTCAATTTTCTTTTCTTTTTTACTTCTTTTTCCTTTTTT
+
1>111@@1>11>01BE11333331311211111//1121211110112211/
@MISEQ:541:000000000-ANU7K:1:1101:14893:1580 2:N:0:
ATGTACATGGATCACAGTTTGCTTGCTCTTCTTCAATATTTGACTTTTTTCT
+
1>1>ADDD311@11F1B133313D101AFBDFF331A3A33221A2B11001
@MISEQ:541:000000000-ANU7K:1:1101:17897:1584 2:N:0:
GCCCAGGTCTTTGTCTTCCTTCTTTCTTTTGTCATCTCCTCTCCTCTTTTTC
+
1111111B111333333311311A3B333A1A3333311101001011A110
@MISEQ:541:000000000-ANU7K:1:1101:16149:1585 2:N:0:
ATTAAGGAGATGCGATGCCATGCATGGCTGTAGCTGCTCTTTCTTGTTACTG
+
1>>1111@1AC@111AA1A11111330AB00122211B11B12DD1DA2222
@MISEQ:541:000000000-ANU7K:1:1101:13135:1586 2:N:0:
GGCTGAGGCAGGAGAATCGCTTTTACTTGCGTTGCGGTGTTTTCAGGTGCCG
+
111>A1BAA?A1A11ABB0ABF0131DF1100000//////A022211110/
@MISEQ:541:000000000-ANU7K:1:1101:17163:1595 2:N:0:
GGGATAAAAAGGAATGTTGCTTATGTACGGACTTCATTTTTTTTTGACACAC
+
11>1A11@111A11BGGG31BA31133D000A0AA2DG2BBAE////A110/
@MISEQ:541:000000000-ANU7K:1:1101:15599:1597 2:N:0:
ACTCAGTGGCAGTCTGGAGCCGGCCTTCCTCTGTGTTGTTCTTCTGTTCCTC
+
1>A>11B31>11F1A311A1100000A101A112220/0A1A1221DDB2D1
@MISEQ:541:000000000-ANU7K:1:1101:13575:1598 2:N:0:
CCTCCCTGATAAGAGTTGTCCCAAAGGGTCGCTTCATTTATCTTCCCCCCCT
+
A>AAAAFFFF3B111BFFGA11110000BB0AAA012222D2B2AAAA/A//
@MISEQ:541:000000000-ANU7K:1:1101:17008:1599 2:N:0:
GTGAATGGGAGACTGGTACTTTCTCTCATTTTTTTATTCTCTTTTTTTCTGT
+
1>>1>@DCFF?AEE11F1B333333311333330001222222111//0122
@MISEQ:541:000000000-ANU7K:1:1101:14913:1599 2:N:0:
TTGAATGGGAGAGTACTCTGCGTTGTTTCCACTTCTTCCTCGTCCCGGCGTT
+
1>11>B31C11111B1FFD3100A0000332111AA1A11A00/////A/A/
@MISEQ:541:000000000-ANU7K:1:1101:14307:1601 2:N:0:
GTGTGAATGGGGTTCTCTGCGTTTATACAATTTTCTACTTCTCCTTATTTAC
+
111>1BDFF111A1BB3F310A000A3A311122212221121111212222
@MISEQ:541:000000000-ANU7K:1:1101:18212:1601 2:N:0:
CAATAAATAAATCTTAAAAATATCAAAAAAACTAAAATTTTCTTTAAACATA
+
>11AA1FFFBBDFF3FB1E111333311000011111211221112211111
@MISEQ:541:000000000-ANU7K:1:1101:16530:1602 2:N:0:
TCTTATATAAGGAGAGCCCCCTTTCCCCTCCTTTTTTTCCTCTTTCTTTTCT
+
1>>A>B3D3B3@111111110001B110BA0BAF1BA/011AA112BD11A1
@MISEQ:541:000000000-ANU7K:1:1101:13045:1602 2:N:0:
GAAGAAATCTGTACGAGCTACCCCATCCTTATTTTCTCTTTTTTCTCACCCC
+
111111BDFFDD331A11111000000A13312A221222111AA122A00/
@MISEQ:541:000000000-ANU7K:1:1101:15570:1602 2:N:0:
TTACTTTCATTGGTACTCCAGTCCATGCAACAAATATTCATTTCTTCACCCG
+
AAAAAFFFFFFB1BBDGFF11A1AA33B11A000A13333A22AA1221100
@MISEQ:541:000000000-ANU7K:1:1101:14068:1602 2:N:0:
GAATGGGGCAGTCGTACTCGGCGTTGATACCACACCTACCATTTCTATTATT
+
111>1@C1AA1CFEFGGGG0000AA0AF2AA1A/B/0100121222222222
@MISEQ:541:000000000-ANU7K:1:1101:13869:1603 2:N:0:
TTTAACAGGAGTGTAGCCATCTTTCTCTGCTCCTTCTGCTCCTTCCTCCTTG
+
11>>113@111B1331BA111133333331311B1BA11B1111A0BA0011
@MISEQ:541:000000000-ANU7K:1:1101:17054:1605 2:N:0:
AAACCAGAGTCATCTGGGGAAATGTAACTCGATCCCATTGAAACATTGGCAT
+
11>A?A1C>@BDFBD1B111101133333D000BB011111111011A101A
@MISEQ:541:000000000-ANU7K:1:1101:16556:1607 2:N:0:
ACCGCAGAGTGACTGGTGTTATATATACACCTACTTCCTTTCCTTCCCATCC
+
1111>111>B1B3BAA11A033333333310010111112211121001100
@MISEQ:541:000000000-ANU7K:1:1101:18064:1607 2:N:0:
CCTTATCTGACCTCTGGCTTTTCTCCCTTGCTGTTACTTCTCTGTTTCCTTT
+
11AAA3BFD31CE1E11AAB1F31AAAF101A1D133321212122B22BE2
@MISEQ:541:000000000-ANU7K:1:1101:16786:1609 2:N:0:
AACGCAGAGTGAATGTGAGTACTCTGCGTTGATACCACTCAAAATTAAACAC
+
11>>AD1DA1@1FFF3A3BBE1FEG310BA00B2DB11100111111111A0
@MISEQ:541:000000000-ANU7K:1:1101:14609:1610 2:N:0:
TGTGACCAGTGATGACACGGGTCTGTGTGTGATGGTTCTCTTTGATCATGAT
+
A1A?A3FFFF1DG33ABA?1000B0D3D0001221BDAAA2DA122D2112D
@MISEQ:541:000000000-ANU7K:1:1101:13501:1611 2:N:0:
GTCAGCCAGTGGCTGCAGACCCTTAGCGGCATTTCGCCTTCAGTTGAGCTTG
+
1>>A>BFFFC11A11AB1110AA011B00A001220///B1112A121A110
@MISEQ:541:000000000-ANU7K:1:1101:14327:1611 2:N:0:
CTAAAAGGGGAACTTCAACTCCATTGAGTTCTCACGCCTCCTTTTGCACGGC
+
>11>>11>A11>FBGG3FGG111AD111DFF3A3A000BA0A1211B21///
@MISEQ:541:000000000-ANU7K:1:1101:13178:1611 2:N:0:
ATATATATGTCTATGCCCCTCTGGTAGACTTAACCTTTACTCTTTTATATGT
+
1>>A?FFFFFDFG3B1FFFC1111B111DBA111111A11112ABB212D22
@MISEQ:541:000000000-ANU7K:1:1101:17881:1612 2:N:0:
TCTCAAAGCAGCCGCTGATGTCTTCCTATCTGCATTTCTCCCCCCTCCACCC
+
11>>13F1>CBBG1AAE0F1A3333113AAF212122222100///A/000/
@MISEQ:541:000000000-ANU7K:1:1101:16279:1613 2:N:0:
CTTCTTGGCTGATCCATCTGCCTTTGTTCCTTCTTCCCCTTTTTCTGCTCCC
+
BBBBBFF4CFAFGFGB5GFE5ABBE5D455A55B5B5B222B333555A5BA
@MISEQ:541:000000000-ANU7K:1:1101:13531:1614 2:N:0:
TTACTAACACAATTTGCTTTCCGTGTTCTTTTTTTTTCTTTTTTTATCTTGT
+
11>>>3@111>11BB333A3111100033BA1100//011111///12DD2D
@MISEQ:541:000000000-ANU7K:1:1101:18008:1614 2:N:0:
TTTGTGACTTCATTGAGACGTATTATCTGAGTGACCCGTTGTAATCCATTAA
+
11>>11FFFF333BFF1FA1E1A133ADD31D113B00000012B2B1DF21
@MISEQ:541:000000000-ANU7K:1:1101:13221:1614 2:N:0:
ATACTGTTGGAAAACGCTTCCTAGAGGCTAATTACTTCCTGTGTCCCTTCCT
+
1>1AAFDFFAB1F1BAE?FA113111000111221DA11B1B1221A1AA01
@MISEQ:541:000000000-ANU7K:1:1101:16820:1614 2:N:0:
TTGTTAAAGGAATCCATCCCTCTTTGATTCTGTTCTCTCCCTTACTAACGTG
+
AA?AA333BF1BBFF1FGF111113333DAD3DB33AAA00AA11D22A0B/
@MISEQ:541:000000000-ANU7K:1:1101:14981:1615 2:N:0:
GGGCACACTCATATGCCGTCTGTGGTTGTCGTCCATGTCTTCACCCAGTTCT
+
11>A1AFFFFFFGGGBDEEEG0D30AA0010A0A0B1DA2FD2A1BF/ABDB
@MISEQ:541:000000000-ANU7K:1:1101:14408:1615 2:N:0:
GTGTGTCTGTCATGAAACCACTCTCTGCATTCCTGACTTCTTCCCCATCTGT
+
1A1AAFFDFFDFF3B1AF111B11AB313AFDAG110B312121AB00BD1D
@MISEQ:541:000000000-ANU7K:1:1101:16414:1616 2:N:0:
CTTCTGTATCATGCCAGGATTTATCATCTTTCCCCACCCTTCTTGCACTGTC
+
>11>11BDFFFF11BA111BBA3DB33A3DDD1B0000000A1A1A1B1021
@MISEQ:541:000000000-ANU7K:1:1101:17385:1617 2:N:0:
GTGTTGGTGAGTGAAGCCATCACGATCCTGTTGGGGCTGTGCCTGCGGTTTT
+
1>AAAAAAAFFFB131BCEAA1100A00B11A100000/B01A110/A////
@MISEQ:541:000000000-ANU7K:1:1101:15349:1617 2:N:0:
GTATATGGAGTGATACCCAAACTCCAGTGCCTTCCACCAACCCACGATGAGG
+
1>1>AFFFFBB?GFGGGGGC11BB1113111AEFGBB00000000/A//110
@MISEQ:541:000000000-ANU7K:1:1101:16880:1617 2:N:0:
CTATTATATAAATCAAAACTTTTTTCCTCCTTATATTCTTGTTGTAAGTTAT
+
>A>AAFFD3F3DF3A111B1AF31A0BF10F1332222AA11100AB2222A
@MISEQ:541:000000000-ANU7K:1:1101:16619:1618 2:N:0:
TCTGTCCTGTGATGTCAGCTTTTCATCGTGTTTTCCACCTCCTTTTTATCTC
+
11>1>FFFDF13A3B33BG1131333D1A0A0B03B310AA0BA2BB0A222
@MISEQ:541:000000000-ANU7K:1:1101:18040:1618 2:N:0:
TCTCTGGTAACTGTATCTACCTCTCTCACCTTTCCCTGTGTTTCTGGAAATT
+
11AAAFFF1BDFGGGGFBD11B1A1BE1DAFEDA1B11A1A0AB221111BD
@MISEQ:541:000000000-ANU7K:1:1101:17608:1619 2:N:0:
CCGTAGCGCCTCATGCCGATGCTCATGCGCGCTCCACCCCCTTCCCCGCCGG
+
1>>A11>A@D1A11A1B0A000B1111A00/////100////0A000//>//
@MISEQ:541:000000000-ANU7K:1:1101:12988:1619 2:N:0:
GCGTGAATGGGTGTACTCTGCGTTGATACAAATACATTTTTTTCTAAAATAA
+
11>AAA?FFF1CEEFGGFG310BE00DA3111111122221//012211211
@MISEQ:541:000000000-ANU7K:1:1101:17675:1620 2:N:0:
TTGCCGGTCCTACTGCTCTTTTTTCTCTCGTTTTCGCTTTTTTCTGCACGGT
+
1>>A11>A@DBBE11B3DG13B10012210000A2///A/B1/0A21A1///
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