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@@ -100,25 +100,97 @@ exports.denovoAssemblage = denovoAssemblage;
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const spadesPath = '/home/thomas/NGS/tools/SPAdes-3.15.0-Linux/bin/spades.py'
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const reads2 = ['/home/thomas/Documents/Programmes/ttest/R1r.fq', '/home/thomas/Documents/Programmes/ttest/R2r.fq']
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const rnames = [
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- 'A00680:166:HYCYGDMXX:1:1356:7663:10723',
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- 'A00680:166:HYCYGDMXX:1:2475:28284:20384',
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- 'A00680:166:HYCYGDMXX:1:1274:10646:6339',
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- 'A00680:166:HYCYGDMXX:1:1314:10303:30921',
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- 'A00680:166:HYCYGDMXX:1:1365:11966:21277',
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- 'A00680:166:HYCYGDMXX:1:1425:21151:6778',
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- 'A00680:166:HYCYGDMXX:1:2288:25301:5822',
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- 'A00680:166:HYCYGDMXX:1:2312:24758:12587',
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- 'A00680:166:HYCYGDMXX:1:2410:17110:13808',
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- 'A00680:166:HYCYGDMXX:1:2410:17761:15468',
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- 'A00680:166:HYCYGDMXX:1:2425:19777:2237',
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- 'A00680:166:HYCYGDMXX:1:2429:13575:20149',
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- 'A00680:166:HYCYGDMXX:2:1374:20971:34773',
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- 'A00680:166:HYCYGDMXX:2:2350:16920:14293',
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- 'A00680:166:HYCYGDMXX:1:2274:12707:16736',
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- 'A00680:166:HYCYGDMXX:1:2274:12717:16720',
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- 'A00680:166:HYCYGDMXX:2:1329:3839:27367',
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- 'A00680:166:HYCYGDMXX:2:1330:1416:7827'
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+ 'A00680:166:HYCYGDMXX:1:1212:20528:10520_1',
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+ 'A00680:166:HYCYGDMXX:2:2184:24442:19680_2',
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+ 'A00680:166:HYCYGDMXX:1:1419:9344:19586_1',
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+ 'A00680:166:HYCYGDMXX:1:1306:14479:14387_1',
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+ 'A00680:166:HYCYGDMXX:2:2184:24442:19680_1',
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+ 'A00680:166:HYCYGDMXX:2:2148:4779:14653',
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+ 'A00680:166:HYCYGDMXX:2:2148:4860:14826',
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+ 'A00680:166:HYCYGDMXX:2:2148:4924:14935',
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+ 'A00680:166:HYCYGDMXX:2:2148:4933:14920',
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+ 'A00680:166:HYCYGDMXX:2:1205:29559:23249_2',
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+ 'A00680:166:HYCYGDMXX:2:1205:29559:23249',
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+ 'A00680:166:HYCYGDMXX:1:1209:1497:28354',
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+ 'A00680:166:HYCYGDMXX:2:2177:24171:24189_1',
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+ 'A00680:166:HYCYGDMXX:2:2221:30635:15875',
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+ 'A00680:166:HYCYGDMXX:2:1336:8034:35916_2',
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+ 'A00680:166:HYCYGDMXX:2:1336:8052:35916_2',
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+ 'A00680:166:HYCYGDMXX:2:1336:8034:35916',
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+ 'A00680:166:HYCYGDMXX:2:1336:8052:35916',
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+ 'A00680:166:HYCYGDMXX:2:1355:24758:35759',
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+ 'A00680:166:HYCYGDMXX:2:1356:27398:2879',
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+ 'A00680:166:HYCYGDMXX:2:1360:31955:31187_2',
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+ 'A00680:166:HYCYGDMXX:1:2342:28999:6715_2',
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+ 'A00680:166:HYCYGDMXX:1:2342:28999:6715',
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+ 'A00680:166:HYCYGDMXX:1:2213:1072:3818_2',
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+ 'A00680:166:HYCYGDMXX:1:2213:1072:3818',
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+ 'A00680:166:HYCYGDMXX:1:2310:10764:5572_2',
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+ 'A00680:166:HYCYGDMXX:1:2442:17671:31407_2',
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+ 'A00680:166:HYCYGDMXX:2:1409:10122:17613_2',
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+ 'A00680:166:HYCYGDMXX:2:1409:10981:19977_2',
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+ 'A00680:166:HYCYGDMXX:2:2414:23764:19038_2',
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+ 'A00680:166:HYCYGDMXX:1:1262:3323:12164',
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+ 'A00680:166:HYCYGDMXX:2:2414:23764:19038',
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+ 'A00680:166:HYCYGDMXX:1:1467:31105:14215',
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+ 'A00680:166:HYCYGDMXX:2:2212:10926:6417',
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+ 'A00680:166:HYCYGDMXX:1:1262:3323:12164_1',
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+ 'A00680:166:HYCYGDMXX:1:1157:13214:20932_2',
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+ 'A00680:166:HYCYGDMXX:1:1157:13223:20948_2',
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+ 'A00680:166:HYCYGDMXX:1:1157:14145:20040_2',
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+ 'A00680:166:HYCYGDMXX:2:1360:2356:14465',
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+ 'A00680:166:HYCYGDMXX:2:1360:2356:14465_1',
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+ 'A00680:166:HYCYGDMXX:1:1220:28492:17237',
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+ 'A00680:166:HYCYGDMXX:1:2220:28782:13573',
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+ 'A00680:166:HYCYGDMXX:2:1448:26024:25958',
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+ 'A00680:166:HYCYGDMXX:2:2420:7175:19774',
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+ 'A00680:166:HYCYGDMXX:2:1317:17372:23437',
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+ 'A00680:166:HYCYGDMXX:2:2420:10673:32002_2',
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+ 'A00680:166:HYCYGDMXX:2:2420:10673:32002',
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+ 'A00680:166:HYCYGDMXX:2:2420:10999:32847_2',
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+ 'A00680:166:HYCYGDMXX:2:2420:10999:32847',
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+ 'A00680:166:HYCYGDMXX:2:2420:9697:32628_2',
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+ 'A00680:166:HYCYGDMXX:2:2420:9697:32628',
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+ 'A00680:166:HYCYGDMXX:2:2229:25012:10582_2',
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+ 'A00680:166:HYCYGDMXX:2:2229:25012:10582',
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+ 'A00680:166:HYCYGDMXX:2:2229:25165:9846_2',
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+ 'A00680:166:HYCYGDMXX:2:2229:25165:9846',
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+ 'A00680:166:HYCYGDMXX:2:2229:25328:10128_2',
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+ 'A00680:166:HYCYGDMXX:2:2229:25328:10128',
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+ 'A00680:166:HYCYGDMXX:2:2229:25165:9846_1',
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+ 'A00680:166:HYCYGDMXX:2:1317:17372:23437_1',
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+ 'A00680:166:HYCYGDMXX:1:2176:11071:20697_2',
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+ 'A00680:166:HYCYGDMXX:1:2176:11071:20697',
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+ 'A00680:166:HYCYGDMXX:2:2132:9534:32064',
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+ 'A00680:166:HYCYGDMXX:1:2105:13187:20165_2',
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+ 'A00680:166:HYCYGDMXX:1:2105:13187:20165',
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+ 'A00680:166:HYCYGDMXX:1:2105:15365:20713',
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+ 'A00680:166:HYCYGDMXX:1:2105:16559:20462',
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+ 'A00680:166:HYCYGDMXX:1:2463:16152:4883_2',
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+ 'A00680:166:HYCYGDMXX:1:2463:18656:8844_2',
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+ 'A00680:166:HYCYGDMXX:2:2318:21694:26224',
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+ 'A00680:166:HYCYGDMXX:2:2318:22209:27993',
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+ 'A00680:166:HYCYGDMXX:2:1319:15908:27320_2',
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+ 'A00680:166:HYCYGDMXX:1:1462:5665:12774_1',
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+ 'A00680:166:HYCYGDMXX:1:2144:14796:8547_1',
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+ 'A00680:166:HYCYGDMXX:1:2144:14796:8547',
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+ 'A00680:166:HYCYGDMXX:1:1149:20139:3270',
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+ 'A00680:166:HYCYGDMXX:1:1149:24343:11490',
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+ 'A00680:166:HYCYGDMXX:1:1458:12228:29434_2',
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+ 'A00680:166:HYCYGDMXX:1:1458:12228:29434',
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+ 'A00680:166:HYCYGDMXX:1:1462:5665:12774',
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+ 'A00680:166:HYCYGDMXX:1:2105:15365:20713_2',
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+ 'A00680:166:HYCYGDMXX:1:2105:16559:20462_2',
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+ 'A00680:166:HYCYGDMXX:1:2144:14796:8547_2',
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+ 'A00680:166:HYCYGDMXX:2:1367:20166:33974_2',
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+ 'A00680:166:HYCYGDMXX:2:2301:7066:16141',
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+ 'A00680:166:HYCYGDMXX:2:2258:4227:16892',
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+ 'A00680:166:HYCYGDMXX:2:2229:25012:10582_1',
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+ 'A00680:166:HYCYGDMXX:2:1228:29939:33176',
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+ 'A00680:166:HYCYGDMXX:1:1425:24975:12587',
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+ 'A00680:166:HYCYGDMXX:1:2450:13874:8265',
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+ 'A00680:166:HYCYGDMXX:2:1367:20166:33974'
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]
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- console.log(await denovoAssemblage(reads2, rnames, spadesPath, console.log));
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-})()
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-*/
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+ const uniq_reads = [...new Set(rnames.map(e => e.split(/_[1-2]$/)[0]))];
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+ console.log(await denovoAssemblage(reads2, uniq_reads, spadesPath, console.log));
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+})()*/
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