diff --git a/pkg/database/migrate/migration b/pkg/database/migrate/migration
new file mode 100755
index 000000000..3e3a2ff63
--- /dev/null
+++ b/pkg/database/migrate/migration
@@ -0,0 +1,30 @@
+#!/usr/bin/env bash
+
+REV=$(date -u +%Y%m%d%H%M%S)
+filename=$1
+
+TAB="$(printf '\t')"
+
+titleize() {
+    echo "$1" | sed -r -e "s/-|_/ /g" -e 's/\b(.)/\U\1/g' -e 's/ //g'
+}
+
+cat > ${REV}_$filename.go << EOF
+package migrate
+
+type rev${REV} struct{}
+
+var $(titleize $filename) = &rev${REV}{}
+
+func (r *rev$REV) Revision() int64 {
+${TAB}return $REV
+}
+
+func (r *rev$REV) Up(op Operation) error {
+${TAB}// Migration steps here
+}
+
+func (r *rev$REV) Down(op Operation) error {
+${TAB}// Revert migration steps here
+}
+EOF
diff --git a/pkg/database/migrate/sqlite.go b/pkg/database/migrate/sqlite.go
index 140988a47..2cec5a026 100644
--- a/pkg/database/migrate/sqlite.go
+++ b/pkg/database/migrate/sqlite.go
@@ -16,15 +16,15 @@ func SQLite(tx *sql.Tx) Operation {
 }
 
 func (s *SQLiteDriver) Exec(query string, args ...interface{}) (sql.Result, error) {
-	return s.Tx.Exec(query, args)
+	return s.Tx.Exec(query, args...)
 }
 
 func (s *SQLiteDriver) Query(query string, args ...interface{}) (*sql.Rows, error) {
-	return s.Tx.Query(query, args)
+	return s.Tx.Query(query, args...)
 }
 
 func (s *SQLiteDriver) QueryRow(query string, args ...interface{}) *sql.Row {
-	return s.Tx.QueryRow(query, args)
+	return s.Tx.QueryRow(query, args...)
 }
 
 func (s *SQLiteDriver) CreateTable(tableName string, args []string) (sql.Result, error) {
@@ -44,17 +44,19 @@ func (s *SQLiteDriver) AddColumn(tableName, columnSpec string) (sql.Result, erro
 }
 
 func (s *SQLiteDriver) DropColumns(tableName string, columnsToDrop []string) (sql.Result, error) {
+	var err error
+	var result sql.Result
 
 	if len(columnsToDrop) == 0 {
 		return nil, fmt.Errorf("No columns to drop.")
 	}
 
-	sql, err := s.getDDLFromTable(tableName)
+	tableSQL, err := s.getDDLFromTable(tableName)
 	if err != nil {
 		return nil, err
 	}
 
-	columns, err := fetchColumns(sql)
+	columns, err := fetchColumns(tableSQL)
 	if err != nil {
 		return nil, err
 	}
@@ -79,6 +81,38 @@ func (s *SQLiteDriver) DropColumns(tableName string, columnsToDrop []string) (sq
 		return nil, fmt.Errorf("No columns match, drops nothing.")
 	}
 
+	// fetch indices for this table
+	oldSQLIndices, err := s.getDDLFromIndex(tableName)
+	if err != nil {
+		return nil, err
+	}
+
+	var oldIdxColumns [][]string
+	for _, idx := range oldSQLIndices {
+		idxCols, err := fetchColumns(idx)
+		if err != nil {
+			return nil, err
+		}
+		oldIdxColumns = append(oldIdxColumns, idxCols)
+	}
+
+	var indices []string
+	for k, idx := range oldSQLIndices {
+		listed := false
+	OIdxLoop:
+		for _, oidx := range oldIdxColumns[k] {
+			for _, cols := range columnsToDrop {
+				if oidx == cols {
+					listed = true
+					break OIdxLoop
+				}
+			}
+		}
+		if !listed {
+			indices = append(indices, idx)
+		}
+	}
+
 	// Rename old table, here's our proxy
 	proxyName := fmt.Sprintf("%s_%s", tableName, uniuri.NewLen(16))
 	if result, err := s.RenameTable(tableName, proxyName); err != nil {
@@ -86,27 +120,40 @@ func (s *SQLiteDriver) DropColumns(tableName string, columnsToDrop []string) (sq
 	}
 
 	// Recreate table with dropped columns omitted
-	if result, err := s.CreateTable(tableName, preparedColumns); err != nil {
+	if result, err = s.CreateTable(tableName, preparedColumns); err != nil {
 		return result, err
 	}
 
 	// Move data from old table
-	if result, err := s.Tx.Exec(fmt.Sprintf("INSERT INTO %s SELECT %s FROM %s;", tableName,
+	if result, err = s.Tx.Exec(fmt.Sprintf("INSERT INTO %s SELECT %s FROM %s;", tableName,
 		strings.Join(selectName(preparedColumns), ", "), proxyName)); err != nil {
 		return result, err
 	}
 
 	// Clean up proxy table
-	return s.DropTable(proxyName)
+	if result, err = s.DropTable(proxyName); err != nil {
+		return result, err
+	}
+
+	// Recreate Indices
+	for _, idx := range indices {
+		if result, err = s.Tx.Exec(idx); err != nil {
+			return result, err
+		}
+	}
+	return result, err
 }
 
 func (s *SQLiteDriver) RenameColumns(tableName string, columnChanges map[string]string) (sql.Result, error) {
-	sql, err := s.getDDLFromTable(tableName)
+	var err error
+	var result sql.Result
+
+	tableSQL, err := s.getDDLFromTable(tableName)
 	if err != nil {
 		return nil, err
 	}
 
-	columns, err := fetchColumns(sql)
+	columns, err := fetchColumns(tableSQL)
 	if err != nil {
 		return nil, err
 	}
@@ -132,6 +179,40 @@ func (s *SQLiteDriver) RenameColumns(tableName string, columnChanges map[string]
 		}
 	}
 
+	// fetch indices for this table
+	oldSQLIndices, err := s.getDDLFromIndex(tableName)
+	if err != nil {
+		return nil, err
+	}
+
+	var idxColumns [][]string
+	for _, idx := range oldSQLIndices {
+		idxCols, err := fetchColumns(idx)
+		if err != nil {
+			return nil, err
+		}
+		idxColumns = append(idxColumns, idxCols)
+	}
+
+	var indices []string
+	for k, idx := range oldSQLIndices {
+		added := false
+	IdcLoop:
+		for _, oldIdx := range idxColumns[k] {
+			for Old, New := range columnChanges {
+				if oldIdx == Old {
+					indx := strings.Replace(idx, Old, New, 2)
+					indices = append(indices, indx)
+					added = true
+					break IdcLoop
+				}
+			}
+		}
+		if !added {
+			indices = append(indices, idx)
+		}
+	}
+
 	// Rename current table
 	proxyName := fmt.Sprintf("%s_%s", tableName, uniuri.NewLen(16))
 	if result, err := s.RenameTable(tableName, proxyName); err != nil {
@@ -139,18 +220,27 @@ func (s *SQLiteDriver) RenameColumns(tableName string, columnChanges map[string]
 	}
 
 	// Create new table with the new columns
-	if result, err := s.CreateTable(tableName, newColumns); err != nil {
+	if result, err = s.CreateTable(tableName, newColumns); err != nil {
 		return result, err
 	}
 
 	// Migrate data
-	if result, err := s.Tx.Exec(fmt.Sprintf("INSERT INTO %s SELECT %s FROM %s", tableName,
+	if result, err = s.Tx.Exec(fmt.Sprintf("INSERT INTO %s SELECT %s FROM %s", tableName,
 		strings.Join(oldColumnsName, ", "), proxyName)); err != nil {
 		return result, err
 	}
 
 	// Clean up proxy table
-	return s.DropTable(proxyName)
+	if result, err = s.DropTable(proxyName); err != nil {
+		return result, err
+	}
+
+	for _, idx := range indices {
+		if result, err = s.Tx.Exec(idx); err != nil {
+			return result, err
+		}
+	}
+	return result, err
 }
 
 func (s *SQLiteDriver) getDDLFromTable(tableName string) (string, error) {
@@ -162,3 +252,32 @@ func (s *SQLiteDriver) getDDLFromTable(tableName string) (string, error) {
 	}
 	return sql, nil
 }
+
+func (s *SQLiteDriver) getDDLFromIndex(tableName string) ([]string, error) {
+	var sqls []string
+
+	query := `SELECT sql FROM sqlite_master WHERE type='index' and tbl_name=?;`
+	rows, err := s.Tx.Query(query, tableName)
+	if err != nil {
+		return sqls, err
+	}
+
+	for rows.Next() {
+		var sql string
+		if err := rows.Scan(&sql); err != nil {
+			// This error came from autoindex, since its sql value is null,
+			// we want to continue.
+			if strings.Contains(err.Error(), "Scan pair: <nil> -> *string") {
+				continue
+			}
+			return sqls, err
+		}
+		sqls = append(sqls, sql)
+	}
+
+	if err := rows.Err(); err != nil {
+		return sqls, err
+	}
+
+	return sqls, nil
+}
diff --git a/pkg/database/migrate/sqlite_test.go b/pkg/database/migrate/sqlite_test.go
index af81588f7..c26d5b9bf 100644
--- a/pkg/database/migrate/sqlite_test.go
+++ b/pkg/database/migrate/sqlite_test.go
@@ -3,6 +3,7 @@ package migrate
 import (
 	"database/sql"
 	"os"
+	"strings"
 	"testing"
 
 	"github.com/russross/meddler"
@@ -117,7 +118,117 @@ func (r *revision4) Revision() int64 {
 	return 4
 }
 
-// ----------
+// ---------- end of revision 4
+
+// ---------- revision 5
+
+type revision5 struct{}
+
+func (r *revision5) Up(op Operation) error {
+	_, err := op.Exec(`CREATE INDEX samples_url_name_ix ON samples (url, name)`)
+	return err
+}
+
+func (r *revision5) Down(op Operation) error {
+	_, err := op.Exec(`DROP INDEX samples_url_name_ix`)
+	return err
+}
+
+func (r *revision5) Revision() int64 {
+	return 5
+}
+
+// ---------- end of revision 5
+
+// ---------- revision 6
+type revision6 struct{}
+
+func (r *revision6) Up(op Operation) error {
+	_, err := op.RenameColumns("samples", map[string]string{
+		"url": "host",
+	})
+	return err
+}
+
+func (r *revision6) Down(op Operation) error {
+	_, err := op.RenameColumns("samples", map[string]string{
+		"host": "url",
+	})
+	return err
+}
+
+func (r *revision6) Revision() int64 {
+	return 6
+}
+
+// ---------- end of revision 6
+
+// ---------- revision 7
+type revision7 struct{}
+
+func (r *revision7) Up(op Operation) error {
+	_, err := op.DropColumns("samples", []string{"host", "num"})
+	return err
+}
+
+func (r *revision7) Down(op Operation) error {
+	if _, err := op.AddColumn("samples", "host VARCHAR(255)"); err != nil {
+		return err
+	}
+	_, err := op.AddColumn("samples", "num INSTEGER")
+	return err
+}
+
+func (r *revision7) Revision() int64 {
+	return 7
+}
+
+// ---------- end of revision 7
+
+// ---------- revision 8
+type revision8 struct{}
+
+func (r *revision8) Up(op Operation) error {
+	if _, err := op.AddColumn("samples", "repo_id INTEGER"); err != nil {
+		return err
+	}
+	_, err := op.AddColumn("samples", "repo VARCHAR(255)")
+	return err
+}
+
+func (r *revision8) Down(op Operation) error {
+	_, err := op.DropColumns("samples", []string{"repo", "repo_id"})
+	return err
+}
+
+func (r *revision8) Revision() int64 {
+	return 8
+}
+
+// ---------- end of revision 8
+
+// ---------- revision 9
+type revision9 struct{}
+
+func (r *revision9) Up(op Operation) error {
+	_, err := op.RenameColumns("samples", map[string]string{
+		"repo": "repository",
+	})
+	return err
+}
+
+func (r *revision9) Down(op Operation) error {
+	_, err := op.RenameColumns("samples", map[string]string{
+		"repository": "repo",
+	})
+	return err
+}
+
+func (r *revision9) Revision() int64 {
+	return 9
+}
+
+// ---------- end of revision 9
 
 var db *sql.DB
 
@@ -305,6 +416,90 @@ func TestMigrateExistingTable(t *testing.T) {
 	}
 }
 
+type sqliteMaster struct {
+	Sql interface{} `meddler:"sql"`
+}
+
+func TestIndexOperations(t *testing.T) {
+	defer tearDown()
+	if err := setUp(); err != nil {
+		t.Fatalf("Error preparing database: %q", err)
+	}
+
+	Driver = SQLite
+
+	mgr := New(db)
+
+	// Migrate, create index
+	if err := mgr.Add(&revision1{}, &revision3{}, &revision5{}).Migrate(); err != nil {
+		t.Errorf("Can not migrate: %q", err)
+	}
+
+	var esquel []*sqliteMaster
+	// Query sqlite_master, check if index is exists.
+	query := `SELECT sql FROM sqlite_master WHERE type='index' and tbl_name='samples'`
+	if err := meddler.QueryAll(db, &esquel, query); err != nil {
+		t.Errorf("Can not find index: %q", err)
+	}
+
+	indexStatement := `CREATE INDEX samples_url_name_ix ON samples (url, name)`
+	if string(esquel[1].Sql.([]byte)) != indexStatement {
+		t.Errorf("Can not find index")
+	}
+
+	// Migrate, rename indexed columns
+	if err := mgr.Add(&revision6{}).Migrate(); err != nil {
+		t.Errorf("Can not migrate: %q", err)
+	}
+
+	var esquel1 []*sqliteMaster
+	if err := meddler.QueryAll(db, &esquel1, query); err != nil {
+		t.Errorf("Can not find index: %q", err)
+	}
+
+	indexStatement = `CREATE INDEX samples_host_name_ix ON samples (host, name)`
+	if string(esquel1[1].Sql.([]byte)) != indexStatement {
+		t.Errorf("Can not find index, got: %s", esquel[0])
+	}
+
+	if err := mgr.Add(&revision7{}).Migrate(); err != nil {
+		t.Errorf("Can not migrate: %q", err)
+	}
+
+	var esquel2 []*sqliteMaster
+	if err := meddler.QueryAll(db, &esquel2, query); err != nil {
+		t.Errorf("Can not find index: %q", err)
+	}
+
+	if len(esquel2) != 1 {
+		t.Errorf("Expect row length equal to %d, got %d", 1, len(esquel2))
+	}
+}
+
+func TestColumnRedundancy(t *testing.T) {
+	defer tearDown()
+	if err := setUp(); err != nil {
+		t.Fatalf("Error preparing database: %q", err)
+	}
+
+	Driver = SQLite
+
+	migr := New(db)
+	if err := migr.Add(&revision1{}, &revision8{}, &revision9{}).Migrate(); err != nil {
+		t.Errorf("Can not migrate: %q", err)
+	}
+
+	var tableSql string
+	query := `SELECT sql FROM sqlite_master where type='table' and name='samples'`
+	if err := db.QueryRow(query).Scan(&tableSql); err != nil {
+		t.Errorf("Can not query sqlite_master: %q", err)
+	}
+
+	if !strings.Contains(tableSql, "repository ") {
+		t.Errorf("Expect column with name repository")
+	}
+}
+
 func setUp() error {
 	var err error
 	db, err = sql.Open("sqlite3", "migration_tests.sqlite")
diff --git a/pkg/database/migrate/util.go b/pkg/database/migrate/util.go
index a0f6bfb59..d2001a071 100644
--- a/pkg/database/migrate/util.go
+++ b/pkg/database/migrate/util.go
@@ -6,12 +6,12 @@ import (
 )
 
 func fetchColumns(sql string) ([]string, error) {
-	if !strings.HasPrefix(sql, "CREATE TABLE ") {
+	if !strings.HasPrefix(sql, "CREATE ") {
 		return []string{}, fmt.Errorf("Sql input is not a DDL statement.")
 	}
 
 	parenIdx := strings.Index(sql, "(")
-	return strings.Split(sql[parenIdx+1:len(sql)-1], ","), nil
+	return strings.Split(sql[parenIdx+1:strings.LastIndex(sql, ")")], ","), nil
 }
 
 func selectName(columns []string) []string {