diff --git a/src/main/java/uk/ac/ebi/ena/readtools/v2/validator/InsdcReadsValidator.java b/src/main/java/uk/ac/ebi/ena/readtools/v2/validator/InsdcReadsValidator.java
index bab4190..14c4894 100644
--- a/src/main/java/uk/ac/ebi/ena/readtools/v2/validator/InsdcReadsValidator.java
+++ b/src/main/java/uk/ac/ebi/ena/readtools/v2/validator/InsdcReadsValidator.java
@@ -11,9 +11,7 @@
 package uk.ac.ebi.ena.readtools.v2.validator;
 
 import htsjdk.samtools.SAMException;
-import java.util.HashSet;
 import java.util.Iterator;
-import java.util.Set;
 import org.apache.commons.lang3.StringUtils;
 import uk.ac.ebi.ena.readtools.v2.FileFormat;
 import uk.ac.ebi.ena.readtools.v2.provider.ReadsProvider;
@@ -22,7 +20,22 @@
 
 public class InsdcReadsValidator extends ReadsValidator {
   public static final String IUPAC_CODES = "ACGTURYSWKMBDHVN.-";
-  private final Set<Character> iupacSet;
+  private static final String AUTCG_CODES = "AUTCG";
+
+  // ASCII lookup tables, case-folded at class-init, so the per-base hot loop needs no
+  // toUpperCase() allocation and no boxed HashSet lookup.
+  private static final boolean[] IUPAC_LOOKUP = buildLookup(IUPAC_CODES);
+  private static final boolean[] AUTCG_LOOKUP = buildLookup(AUTCG_CODES);
+
+  private static boolean[] buildLookup(String codes) {
+    boolean[] table = new boolean[128];
+    for (char c : codes.toCharArray()) {
+      table[Character.toUpperCase(c)] = true;
+      table[Character.toLowerCase(c)] = true;
+    }
+    return table;
+  }
+
   private static final int MIN_QUALITY_SCORE = 30;
 
   public static String ERROR_NULL_READS = "Reads cannot be null";
@@ -47,11 +60,6 @@ public class InsdcReadsValidator extends ReadsValidator {
 
   public InsdcReadsValidator(long readCountLimit) {
     super(readCountLimit);
-
-    iupacSet = new HashSet<>();
-    for (char c : IUPAC_CODES.toCharArray()) {
-      iupacSet.add(c);
-    }
   }
 
   public long getReadCount() {
@@ -127,15 +135,39 @@ public boolean validate(ReadsProviderFactory readsProviderFactory)
         }
 
         basesCount += effectiveBases.length();
-        for (char base : effectiveBases.toUpperCase().toCharArray()) {
-          if (iupacSet.contains(base)) {
-            if (base == 'A' || base == 'U' || base == 'T' || base == 'C' || base == 'G') {
-              autcgCount++;
+        // Fast path: pure-ASCII bases, checked against case-folded lookup tables with no
+        // allocation. Non-ASCII bases fall back to the original String.toUpperCase() path so
+        // that exotic case-folding (e.g. U+017F LATIN SMALL LETTER LONG S -> 'S') keeps
+        // behaving exactly as before.
+        int readAutcgCount = 0;
+        boolean nonAscii = false;
+        for (int i = 0, len = effectiveBases.length(); i < len; i++) {
+          char base = effectiveBases.charAt(i);
+          if (base >= 128) {
+            nonAscii = true;
+            break;
+          }
+          if (IUPAC_LOOKUP[base]) {
+            if (AUTCG_LOOKUP[base]) {
+              readAutcgCount++;
             }
           } else {
             throw new ReadsValidationException(ERROR_NOT_IUPAC, readCount, effectiveBases);
           }
         }
+        if (nonAscii) {
+          readAutcgCount = 0;
+          for (char base : effectiveBases.toUpperCase().toCharArray()) {
+            if (IUPAC_CODES.indexOf(base) >= 0) {
+              if (AUTCG_CODES.indexOf(base) >= 0) {
+                readAutcgCount++;
+              }
+            } else {
+              throw new ReadsValidationException(ERROR_NOT_IUPAC, readCount, effectiveBases);
+            }
+          }
+        }
+        autcgCount += readAutcgCount;
 
         int totalQuality = 0;
         for (char q : effectiveQualityScores.toCharArray()) {
diff --git a/src/main/java/uk/ac/ebi/ena/readtools/v2/validator/PairedFastqReadsValidator.java b/src/main/java/uk/ac/ebi/ena/readtools/v2/validator/PairedFastqReadsValidator.java
index bcdbdce..9cb4267 100644
--- a/src/main/java/uk/ac/ebi/ena/readtools/v2/validator/PairedFastqReadsValidator.java
+++ b/src/main/java/uk/ac/ebi/ena/readtools/v2/validator/PairedFastqReadsValidator.java
@@ -70,57 +70,31 @@ protected void extraReadsValidation(ReadStyle readStyle, long readCount, FastqRe
     addCount++;
 
     if (pairingBloomWrapper != null && labels != null) {
+      // Name and index are derived from the same regex match, so match once and read both
+      // groups rather than running the same patterns twice per read.
+      String readName = read.getName();
       if (readStyle == ReadStyle.CASAVA18) {
-        pairingBloomWrapper.add(getCasavaReadNameWithoutIndex(read.getName(), readCount));
-        labels.add(getCasavaReadIndex(read.getName(), readCount));
+        Matcher matcher = P_CASAVA_18_NAME.matcher(readName);
+        if (!matcher.matches()) {
+          throw new ReadsValidationException(
+              String.format("Line [%s] does not match %s regexp", readName, ReadStyle.CASAVA18),
+              readCount);
+        }
+        pairingBloomWrapper.add(matcher.group(1));
+        labels.add(matcher.group(3));
       } else {
-        pairingBloomWrapper.add(getNonCasavaReadNameWithoutIndex(read.getName()));
-        labels.add(getNonCasavaReadIndex(read.getName()));
+        String nameWithoutIndex = readName;
+        String index = providerName;
+        if (!CASAVA_LIKE_EXCLUDE_REGEXP.matcher(readName).find()) {
+          Matcher m = SPLIT_REGEXP.matcher(readName);
+          if (m.find()) {
+            nameWithoutIndex = m.group(1);
+            index = m.group(2);
+          }
+        }
+        pairingBloomWrapper.add(nameWithoutIndex);
+        labels.add(index);
       }
     }
   }
-
-  private String getCasavaReadNameWithoutIndex(String readName, long readIndex)
-      throws ReadsValidationException {
-    Matcher matcher = P_CASAVA_18_NAME.matcher(readName);
-    if (!matcher.matches()) {
-      throw new ReadsValidationException(
-          String.format("Line [%s] does not match %s regexp", readName, ReadStyle.CASAVA18),
-          readIndex);
-    }
-    return matcher.group(1);
-  }
-
-  private String getCasavaReadIndex(String readName, long readIndex)
-      throws ReadsValidationException {
-    Matcher matcher = P_CASAVA_18_NAME.matcher(readName);
-    if (!matcher.matches()) {
-      throw new ReadsValidationException(
-          String.format("Line [%s] does not match %s regexp", readName, ReadStyle.CASAVA18),
-          readIndex);
-    }
-    return matcher.group(3);
-  }
-
-  private String getNonCasavaReadNameWithoutIndex(String readName) {
-    Matcher casavaLikeMatcher = CASAVA_LIKE_EXCLUDE_REGEXP.matcher(readName);
-    if (!casavaLikeMatcher.find()) {
-      Matcher m = SPLIT_REGEXP.matcher(readName);
-      if (m.find()) {
-        return m.group(1);
-      }
-    }
-    return readName;
-  }
-
-  private String getNonCasavaReadIndex(String readName) {
-    Matcher casavaLikeMatcher = CASAVA_LIKE_EXCLUDE_REGEXP.matcher(readName);
-    if (!casavaLikeMatcher.find()) {
-      Matcher m = SPLIT_REGEXP.matcher(readName);
-      if (m.find()) {
-        return m.group(2);
-      }
-    }
-    return providerName;
-  }
 }