diff --git a/README.md b/README.md
index 6d25113..ee45c64 100644
--- a/README.md
+++ b/README.md
@@ -123,8 +123,10 @@ results/
 │   ├── map-to-remove/
 │   │   ├── <sample_name>.mapped.fastq.gz
 │   │   ├── <sample_name>.unmapped.fastq.gz
-│   │   ├── <sample_name>.mapped.bam
-│   │   ├── <sample_name>.unmapped.bam
+│   │   ├── <sample_name>.sorted.bam
+│   │   ├── <sample_name>.sorted.bam.bai
+│   │   ├── <sample_name>.sorted.flagstat.txt
+│   │   ├── <sample_name>.sorted.idxstats.tsv
 │   │   ├── strict-dcs/
 │   │   │   ├── <sample_name>.no-dcs.bam
 │   │   │   ├── <sample_name>.true-dcs.bam
@@ -132,18 +134,22 @@ results/
 │   │   └── soft-clipped/
 │   │       ├── <sample_name>.soft-clipped.bam
 │   │       └── <sample_name>.passed-clipped.bam
-│   └── map-to-keep/
-│       ├── <sample_name>.mapped.fastq.gz
-│       ├── <sample_name>.unmapped.fastq.gz
-│       ├── <sample_name>.mapped.bam
-│       ├── <sample_name>.unmapped.bam
-│       ├── strict-dcs/
-│       │   ├── <sample_name>.no-dcs.bam
-│       │   ├── <sample_name>.true-dcs.bam
-│       │   └── <sample_name>.false-dcs.bam
-│       └── soft-clipped/
-│           ├── <sample_name>.soft-clipped.bam
-│           └── <sample_name>.passed-clipped.bam
+│   ├── map-to-keep/
+│   │   ├── <sample_name>.mapped.fastq.gz
+│   │   ├── <sample_name>.unmapped.fastq.gz
+│   │   ├── <sample_name>.sorted.bam
+│   │   ├── <sample_name>.sorted.bam.bai
+│   │   ├── <sample_name>.sorted.flagstat.txt
+│   │   ├── <sample_name>.sorted.idxstats.tsv
+│   │   ├── strict-dcs/
+│   │   │   ├── <sample_name>.no-dcs.bam
+│   │   │   ├── <sample_name>.true-dcs.bam
+│   │   │   └── <sample_name>.false-dcs.bam
+│   │   └── soft-clipped/
+│   │       ├── <sample_name>.soft-clipped.bam
+│   │       └── <sample_name>.passed-clipped.bam
+|   ├── host.fa.fai
+|   └── host.fa.gz
 ├── logs/*.html
 └── qc/multiqc_report.html
 ```
@@ -152,6 +158,10 @@ The most important files you are likely interested in are `results/clean/<sample
 
 For debugging purposes we also provide various intermediate results in the `intermediate/` folder.
 
+## Acknowledgements
+
+Thanks to Matt Huska (@matthuska) for extensive testing of `CLEAN`, bug fixing, and reorganizing the output.
+
 ## Citations
 
 If you use `CLEAN` in your work, please consider citing our preprint:
diff --git a/modules/utils.nf b/modules/utils.nf
index 5d94aad..6b4e001 100644
--- a/modules/utils.nf
+++ b/modules/utils.nf
@@ -106,6 +106,8 @@ process filter_fastq_by_name {
             fn.matches('.*.mapped_merged_merged.fast[aq].gz$') ? "removed/${fn}".replaceAll(~'.mapped_merged_merged(.fast[aq].gz)$', '$1') :
             fn.matches('.*.fast[aq].clean.fast[aq].gz$') ? "clean/${fn}".replaceAll(~'.fast[aq].clean(.fast[aq].gz)$', '$1') :
             fn.matches('.*.fast[aq].contamination.fast[aq].gz$') ? "removed/${fn}".replaceAll(~'.fast[aq].contamination(.fast[aq].gz)$', '$1') :
+            fn.matches('.*.unmapped_(1|2|singleton).fast[aq].gz$') ? "clean/${fn}".replaceAll(~'.unmapped_(1|2|singleton)(.fast[aq].gz)$', '_$1$2') :
+            fn.matches('.*.mapped_(1|2|singleton).fast[aq].gz$') ? "removed/${fn}".replaceAll(~'.mapped_(1|2|singleton)(.fast[aq].gz)$', '_$1$2') :
             fn
       }
     )