diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index ac6d9a68..36289e56 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -40,7 +40,7 @@ repos:
 #         log_file: mypy.log
 
 -   repo: https://github.com/pycqa/flake8
-    rev: 7.1.1
+    rev: 7.1.2
     hooks:
     -   id: flake8
         args: [
diff --git a/amira/__init__.py b/amira/__init__.py
index 364e7bae..7bbb2ef5 100644
--- a/amira/__init__.py
+++ b/amira/__init__.py
@@ -1 +1 @@
-__version__ = "0.6.4"
+__version__ = "0.6.5"
diff --git a/amira/__main__.py b/amira/__main__.py
index d8fb0ec0..6e25ef86 100644
--- a/amira/__main__.py
+++ b/amira/__main__.py
@@ -2,6 +2,7 @@
 import json
 import os
 import random
+import re
 import sys
 import time
 
@@ -24,7 +25,7 @@
     process_reference_alleles,
     run_pandora_map,
 )
-from amira.read_utils import parse_fastq, plot_read_length_distribution
+from amira.read_utils import parse_fastq, plot_read_length_distribution, write_fastq
 from amira.result_utils import (
     estimate_copy_numbers,
     filter_results,
@@ -260,15 +261,16 @@ def main() -> None:
     if not args.quiet:
         sys.stderr.write("\nAmira: loading FASTQ file.\n")
     fastq_content = parse_fastq(args.reads)
+    # remove underscores in read names
+    fastq_content = {re.sub(r"\W+", "", r): fastq_content[r] for r in fastq_content}
+    # write the modified fastq data to the output directoy
+    read_fastq_path = os.path.join(args.output_dir, os.path.basename(args.reads))
+    write_fastq(
+        read_fastq_path,
+        fastq_content,
+    )
     # run pandora
     if args.pandoraSam is None and args.pandoraJSON is None:
-        # if args.sample_reads:
-        #     # randomly sample 100,000 reads
-        #     read_fastq_path = downsample_reads(
-        #         fastq_content, args.reads, args.output_dir, args.sample_size
-        #     )
-        # else:
-        read_fastq_path = args.reads
         if not args.quiet:
             sys.stderr.write("\nAmira: running Pandora map.\n")
         pandoraSam, pandoraConsensus = run_pandora_map(
@@ -282,9 +284,6 @@ def main() -> None:
     else:
         pandoraSam = args.pandoraSam
         pandoraConsensus = args.pandoraConsensus
-        read_fastq_path = args.reads
-    # remove underscores in read names
-    fastq_content = {r.replace("_", ""): fastq_content[r] for r in fastq_content}
     # import a JSON of genes on reads
     if args.pandoraJSON:
         if not args.quiet:
@@ -564,7 +563,7 @@ def main() -> None:
     copy_numbers = estimate_copy_numbers(
         mean_read_depth,
         os.path.join(args.output_dir, "AMR_allele_fastqs", "longest_reads.fasta"),
-        args.reads,
+        read_fastq_path,
         args.cores,
         args.samtools_path,
     )
diff --git a/amira/pre_processing.py b/amira/pre_processing.py
index 9f71be2c..46af5566 100644
--- a/amira/pre_processing.py
+++ b/amira/pre_processing.py
@@ -12,8 +12,9 @@
 def run_pandora_map(pandora_path, panRG_path, readfile, outdir, cores, seed):
     command = f"{pandora_path} map -t {cores} --min-gene-coverage-proportion 0.5 --max-covg 10000 "
     command += (
-        f"-o {os.path.join(outdir, 'pandora_output')} {panRG_path} {readfile} --rng-seed {seed}"
+        f"-o {os.path.join(outdir, 'pandora_output')} {panRG_path} {readfile} --rng-seed {seed} "
     )
+    command += "--min-abs-gene-coverage 1"
     # check that the panRG file exists
     if not os.path.exists(panRG_path):
         sys.stderr.write("\nAmira: panRG file does not exist.\n")
diff --git a/pyproject.toml b/pyproject.toml
index 15f6c9a4..34e36694 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "amira-amr"
-version = "0.6.4"
+version = "0.6.5"
 description = "Amira"
 authors = ["Daniel Anderson <dander@ebi.ac.uk>"]
 license = "Apache-2.0"